title: AMM2 STM3466

type: mixed

city: Rockville

first: Bryan

last: Frank

state: MD

address: 9704 Medical Center Drive

department: Dept of Infectious Diseases

institute: The J. Craig Venter Institute

description: normalized using 14028s total RNA isolated from the equvalent condition.

hyb_protocol: A hybridization mixture containing the same amounts of Cy3 and Cy5-labeled probes was applied to a non-redundant pan-Salmonella orf array and incubated in a hybridization chamber (Corning) at 42°C overnight.

scan_protocol: Each array slide has identical triplicate arrays as technical replicates. Slides hybridized with Cy3/Cy5-labled probes were scanned using ScanArray Express (Packard Bioscience, BioChip Technologies) and the fluorescent signal intensities were quantified using QuantArray 3.0 software (Packard Bioscience, BioChip Technologies) with adaptive quantification.

data_processing:
The raw data was processed in WebArray (Xia X et al. 2005 BMC Bioinformatics 6: 306) for statistical normalization. print-tip loess normalization method was applied.
Value was standardized by the intensity of wild type RNA prepared from the equivalent condition using the formula of log2 ratio (test/reference).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: AMM2 condition 4 h

label_protocol: Total RNAs were reverse transcribed with random hexamers and Superscript II (Invitrogen) and subsequent reverse transcripts were labeled by Cy3-linked dCTP (Amersham Biosciences). Genomic DNA from 14028s was isolated using GeneElute bacterial genomic DNA kit (Sigma) and labeled with Cy5-linked dCTP (Amersham Biosciences) as reference for hybridization.

growth_protocol: Bacteria were grown under four different conditions to cover expression of a large number of Salmonella genes. They were: log phase in Luria-Bertani (LB) medium, stationary phase in LB medium, acidic minimal media 1 (AMM1; grown in AMM media overnight, diluted 1:100 and grown for an additional 4 hrs) and AMM2 (grown in LB to stationary phase and resuspended in the same volume of acidic minimal media [Yoon H et al. 2009 PLoS Pathog 5(2):e1000306]). The latter two media partially mimic the intracellular environment of the Salmonella containing vacuole and differ from each other only in the pre-growth conditions. Because of the density of the culture and the fact that the bacteria are in stationary phase the bacteria do not grow in AMM2. The formula for AMM (pH 5.0) is 100 mM Tris-Cl, 5 mM KCl, 7.5 mM (NH4)2SO4, 0.5 mM K2SO4, 1 mM KH2PO4, 0.2% glycerol, 0.1% casamino acids, and 8 µM MgCl2.

extract_protocol: RNAprotect Bacteria Reagent (Qiagen)-pretreated cells were processed using Qiagen RNeasy midi kit (Qiagen) in combination with DNase I (Qiagen) treatment. For genomic DNA preparation, GeneElute bacterial genomic DNA kit (Sigma) was used.

treatment_protocol: Cells were cultivated in four conditions as described above in triplicate and lysed following the instructions of Qiagen RNeasy midi kit (Qiagen) in combination with DNase I (Qiagen) treatment. Cells were treated with RNAprotect Bacteria Reagent (Qiagen) before RNA extraction.

source_name: LB stationary phase 18 h


title: AMM2 STM2924

status: Public on May 31 2012

country: USA

molecule: total RNA

tag: genotype/variation

molecule: genomic DNA

value: wild type


title: Oxidative stress 4 hour_OS4h2

type: RNA

city: New Delhi

first: Anil

last: Grover

state: Delhi

address: Benito Juarez Road

department: Plant Molecular Biology

country: India

institute: University of Delhi South Campus

description: Oxidative stress 4 hour replicate 2

hyb_protocol: Hybridization and wash processes were performed according to the manufacturer’s instructions.

scan_protocol: Hybridized microarrays were scanned using agilent microarray scanner (g2505b, agilent technologies, usa) at 5µ resolution.

data_processing: Feature extraction software (version 9.5.1 Agilent Technologies, USA) was employed for the image analysis and data extraction process. The normalization was done using GeneSpring GX 7.3.1(Agilent Technologies, USA) using the recommended Per Chip and Per Gene Data Transformation: Set measurements less than 0.01 to 0.01, Per Chip: Normalize to 50th percentile Per Gene: Normalize to Specific Samples (Treated Vs Control). Data analysis was done using GeneSpring GX version 7.3.1 (Agilent Technologies, USA) and Microsoft Excel. In total three biological replicates were processed in a similar manner for the microarray analysis.  Genes showing differential expression (up or down) by 2 fold or more (log2 values) with a p- value of  0.05 were considered statistically significant.

organism: Oryza sativa Indica Group

source_name: Oxidative stress 4 hour

label_protocol: Total RNA (200ng) was labeled with Cy3 using Agilent Low RNA Input fluorescent Linear Amplification Kit (Agilent Technologies).

growth_protocol: Seedlings were grown at 28+2oC and 14 h light/ 10 h dark cycle maintained in growth room (light intensity ~250µmol.m-2.s-2, humidity 40-50%) for 10 d.

extract_protocol: Total RNA was isolated from ~100 mg tissue using Tri- Reagent (Sigma, USA) as per the manufacturer’s instructions, and further purified using RNAesy Mini Elute Kit (Qiagen).

treatment_protocol: Uniformly grown seedlings (10 day old) were transferred to beakers, which contain distilled water maintained at 42+1oC for heat stress (HS) for 10 and 30 minutes. Similarly, seedlings were transferred to beakers, which contain distilled water maintained at 5+1oC for cold stress (CS) for 1 and 5h. Uniformly grown seedlings (were transferred to beakers, which contain 10mM H2O2 at 28+2oC for oxidative stress (OS) for 1 and 4 h. All samples were harvested, frozen in liquid nitrogen and kept at -80°C immediately after stress treatment.

tag: cultivar

value: Pusa Basmati (PB1)

tag: age

value: 10-day old

tag: tissue type

value: whole seedling

tag: stress type

value: Oxidative stress

tag: time point

value: 4 hour


title: 3LD+T.HVC replicate 3 [e01]

city: Urbana

first: Kirstin

last: Replogle

state: IL

address: 1206 W Gregory Drive

institute: University of Illinois

hyb_protocol: Samples were suspended in SlideHyb#1 (Ambion), applied to slides in Corning Hybridization Chambers, and incubated O/N at 42C. After hybridization, the slides were washed sequentially in 1X SSC, 0.2% SDS; 0.1X SSC, 0.2% SDS; and 0.1X SSC for 5 minutes each, and spun dry.

scan_protocol: Scanned on an Axon GenePix 4000B scanner Images were quantified using Axon GenePix 6.0.

data_processing: Data were background-subtracted and values < 0.5 were set to 0.5. Spots with -100 flags were filtered out before print-tip loess normalization. A scale between-array normalization was performed, then arrays with the reference in the Cy5 channel were inverted by multiplying by -1 to make all log ratios test/reference.

organism: Taeniopygia guttata

source_name: universal SoNG reference

label_protocol: 1 µg of aRNA was primed with 3 µl of 100 µM random hexamer primers at 70C for 10 min, then reversed transcribed at 42C for 16 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM dATP, dCTP, dGTP, 60µM dTTP and 40µM aa-dUTP; RNA was hydrolyzed in the presence of NaOH and EDTA and samples were cleaned up on a spin column. Finally, Cy3 and Cy5 dye esters (GE Healthcare) were coupled to aa-dUTP residues in NaCO3 buffer for 2 hrs at room temp, then neutralized and cleaned on spin columns.

extract_protocol: Experimental samples: Total RNA was extracted using Absolutely RNA Microprep kit (Stratagene). 200ng total RNA was double-amplified using MessageAmp II aRNA kit (Ambion). Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: Gambel's White crowned sparrows were castrated and synchronized to a Short Day (SD) state to ensure regressed song nuclei, basal levels of Testosterone (T) typical of the non-breeding season, low song rates and unstereotyped song structure, and a low intrinsic spontaneous firing rate in the robust nucleus of the arcopalluim (RA). Then, on Day 0 of the experiment we sacrificed 6 birds. This group of birds, referred to as SD long-term, represents the steady-state of the regressed song control system and served as a baseline for all other groups. We implanted the rest of the birds with a subcutaneous Silastic capsule of T, and shifted them to Long Day (LD) photoperiod. To measure gene expression while the song control system was actively changing from a nonbreeding to a breeding phenotype, 6 birds were sacrificed on each of days 3, 7, and 21 (3LD+T, 7LD+T, and 21LD+T, respectively). By day 21, the song control system has reached its full breeding phenotype, and this time point represents the breeding-state song control system. On Day 21, the subcutaneous T capsules were removed from the remaining birds and they were shifted overnight to SD photoperiod to induce regression of the song control system back to the non-breeding state. On each of days 22 and 23 we sacrificed 6 birds (1SD-T and 2SD-T, respectively) to measure gene expression while the song control system is actively regressing. To control for circadian patterns of gene expression, all birds were sacrificed during the three hour period following their subjective dawn (i.e., lights on).

tag: gender

value: male and female

tag: tissue

value: telencephalon

tag: light

value: Dark cycle:NA

tag: testosterone at sacrifice

tag: treatment protocol

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country

organism: Zonotrichia leucophrys gambelii

value: male

value: HVC

value: Dark cycle:20:4

value: Yes

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 3 days.


title: AMM2 STM1753


title: AMM2 STM4361


title: AMM2 STM2640


title: AMM2 STM2688


title: hippocampus_medip_abuse_26_rep1

type: genomic

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

description:
26_medip_1
Comparison of hippocampus DNA methylation in humans with and without a history of childhood abuse.

hyb_protocol: All of the steps of hybridization and washing were performed following the Agilent protocol for ChIP-on-chip analysis.

scan_protocol: Scanning was performed using the Agilent Technologies Scanner G2505B.

data_processing: The data were background subtracted, and quantile normalized in R using the limma package from the Bioconductor project.

organism: Homo sapiens

source_name: hippocampus, MeDIP, abuse group

label_protocol: 2ug of each of the input and bound fractions were labeled for the microarray hybridization. Cy3-dUTP and Cy5-dUTP (Perkin Elmer) were used to label the input and the bound fractions, respectively. Cot-1 DNA was added to the hybridization mix to minimize cross-hybridization between repetitive elements.

extract_protocol: Samples were dissected at 4C, snap-frozen on dry ice, and stored in plastic vials at -80C until analysis. DNA (2.g) was sonicated on ice for a total of 3 min, using 5 sec pulses with 15 sec resting times, to fragment the DNA to between 200 bp and 700 bp, as verified subsequently on a 1.5% agarose gel. After denaturing, 1/10th of each sample was removed as input DNA. The remainder of the sample was then precleared with sepharose beads, bound to anti-5 methylcytosine antibody (Calbiochem), washed, and eluted. PCR was performed to assess relative enrichment of an unmethylated plasmid DNA (GFP) versus an in vitro methylated plasmid DNA (Luciferase). Samples were PCR purified (GenScript) and quantified by Nanodrop, and for each sample, 100ng of input and immunoprecipitated DNA were subjected to whole genome amplification (Sigma). Samples were again quantified to assess the results of WGA, and then labeled with Cy3 (Input) or Cy5 (meDIP) prior to hybridization to the microarray.

value: hippocampus

tag: group

value: abuse

tag: individual identifier

tag: medip antibody

value: anti-5 methylcytosine antibody

tag: antibody vendor

value: Calbiochem

tag: antibody catalog number

tag: antibody lot#

source_name: hippocampus, input DNA, abuse group


title: AMM2 STM2826

tag: genotype/variation

value: wild type


title: Oxidative stress 4 hour_OS4h1

description: Oxidative stress 4 hour replicate 1

tag: cultivar

value: Pusa Basmati (PB1)

value: 10-day old

value: whole seedling


title: Heat shock 10 min_HS101

description: Heat shock 10 min replicate 1

source_name: Heat shock 10 min

tag: age

value: Heat shock

value: 10 min


title: AMM2 STM3501


title: AMM2 STM1391


title: Heat shock 10 min_HS103

description: Heat shock 10 min replicate 3

tag: tissue type


title: Heat shock 10 min_HS102

description: Heat shock 10 min replicate 2

tag: stress type


title: Oxidative stress 4 hour_OS4h3

description: Oxidative stress 4 hour replicate 3

value: Oxidative stress

tag: time point

value: 4 hour


title: Heat shock 30 min_HS302

description: Heat shock 30 min replicate 2

source_name: Heat shock 30 min

value: 30 min


title: AMM2 STM1444


title: AMM2 STM0982


title: AMM2 STM1230


title: AMM2 PSLT041


title: Heat shock 30 min_HS303

description: Heat shock 30 min replicate 3


title: AMM2 STM0118


title: AMM1 STM3501

source_name: AMM1 condition 4 h


title: AMM1 STM4361


title: Control_Cont3

description: Control replicate 3

source_name: Control

value: Control


title: AMM1 STM2826


title: Heat shock 30 min_HS301

description: Heat shock 30 min replicate 1


title: Control_Cont2

description: Control replicate 2


title: AMM1 STM2640


title: AMM1 STM1444


title: AMM1 STM1753


title: Control_Cont1

description: Control replicate 1


title: AMM1 STM2924


title: AMM1 STM1391


title: Oxidative stress 1 hour_OS1h3

description: Oxidative stress 1 hour replicate 3

source_name: Oxidative stress 1 hour

value: 1 hour


title: Cold shock 5 hour_C5h1

description: Cold shock 5 hour replicate 1

source_name: Cold shock 5 hour

value: Cold shock

value: 5 hour


title: Cold shock 1 hour_C1h2

description: Cold shock 1 hour replicate 2

source_name: Cold shock 1 hour


title: Oxidative stress 1 hour_OS1h1

description: Oxidative stress 1 hour replicate 1


title: Cold shock 1 hour_C1h1

description: Cold shock 1 hour replicate 1


title: Cold shock 1 hour_C1h3

description: Cold shock 1 hour replicate 3


title: Cold shock 5 hour_C5h2

description: Cold shock 5 hour replicate 2


title: Cold shock 5 hour_C5h3

description: Cold shock 5 hour replicate 3


title: Oxidative stress 1 hour_OS1h2

description: Oxidative stress 1 hour replicate 2


title: AMM1 STM2688


title: AMM1 STM0982


title: AMM1 STM1230


title: AMM1 STM0118


title: LB stationary STM4361


title: LB stationary STM3501


title: AMM1 PSLT041


title: LB stationary STM3466


title: MHCC97-H c-Met shRNA (7165895058_H)

city: Hershey

first: Penn State

last: COM

state: PA

address: 500 University Drive

department: Genome Sciences Facility

institute: Penn State College of Medicine

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using average normalization with GenomeStudio V2011.1 Version 1.9.0

source_name: Liver

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

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

treatment_protocol: Stable knockdown of Scrambled control, c-Met and CD44s was generated using MHCC97-H cells. Scrambled, CD44s or c-Met shRNA was transfected into cells for 48 hours using Fugene. After 48 hours, medium was changed and puromycin or zeocin was added to select for clones. After two weeks, pooled clones of Scrambled control and single clones of c-Met shRNA was passaged for analysis.

tag: cell line

value: HCC

tag: transvector

value: c-Met shRNA


title: MHCC97-H CD44s shRNA (7165895058_K)

description: Replicate 3

value: CD44 shRNA


title: MHCC97-H Scrm shRNA (7165895079_J)

description: Replicate 1

value: scrambled shRNA


title: LB stationary STM2826

value: wild type


title: MHCC97-H CD44s shRNA (7165895079_G)

description: Replicate 1


title: LB stationary STM2924


title: MHCC97-H c-Met shRNA (7165895058_L)

description: Replicate 3


title: MHCC97-H Scrm shRNA (7165895058_C)

description: Replicate 3


title: brain zebra finch12 rep4

city: Durham

first: Miriam

middle: Virtudes

last: Rivas

state: NC

address: 451 Bryan Research Building

department: Neurobiology

institute: Duke University Medical Center

description: gene expression brain

hyb_protocol: From the amplified cDNA reactions, 1.5 mg of amplified labeled product (probe) was denatured and hybridized to our custom designed songbird oligo spotted arrays (Agilent Technologies; Whitney et al, in preparation) containing oligos designed from over 44,000 relatively unique cDNA transcripts, including some splice variants. More detailed information on the arrays is available at http://aviangenomes.org/main/zebrafincholigoarray.

scan_protocol: After hybridization, the microarrays were scanned with the Axon GenePix 4000B scanner to acquire and analyze the expression data (Molecular Devices).

data_processing: For analysis, signal intensity on an axon array scanner was obtained in Agilent oligoarray format. The data was extracted in R using the Agi4x44PreProcess Bioconductor library. The values were normalized using median centered log2 transformation. Raw and normalized expression distributions were evaluated for sample quality control using the normalization centering profile, the normalization factor, and a cross-sample correlation analysis. Normalization was evaluated with VSN (variance stabilization normalization)-Scale Factor package in R (R Foundation for Statistical Computing, Vienna, Austria). VSN-Scale Factor was chosen because it performed the least manipulation of the original intensity profiles, and normalizes samples among themselves.

source_name: 12 zebra finch

label_protocol: Samples were labeled with Cy3-dCTP using the uMACS SuperAmp Kit (Miltenyi Biotec).

extract_protocol: After laser capture of the samples onto the CapSure HS LCM caps (Molecular Devices), the membrane withcaptured brain nuclei was carefully peeled away from the cap and placed in a 0.65 ml tube of the PicoPure RNA isolation kit which contained 50ul of disruption buffer (Molecular Devices). Tubes were placed on a 42oC heat block for 30 min then placed in a -80 oC freezer until all desired samples were captured. Total RNA was then isolated according to the remaining protocol steps in the PicoPure isolation kit instructions (Molecular Devices). The concentration and integrity of total RNA were measured on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA USA) using the RNA Pico 6000 kit according to manufacturer instructions (Agilent Technologies).

tag: cell type

value: 12th Motor Neuron

tag: gender

value: Male

value: Adult

tag: organism

value: Zebra Finch


title: MHCC97-H c-Met shRNA (7166142057_H)

description: Replicate 1


title: MHCC97-H Scrm shRNA (7165895079_L)

description: Replicate 2


title: 293 p65S547A Etop8h repl3

city: Liege

first: Helene

last: Sabatel

address: avenue de l'hopital

country: Belgium

institute: Universite de Liege

description:
SAMPLE 18
replicate 3

data_processing: The data were normalised using quantile normalisation with Genome Studio software

source_name: HEK293 p65S547A 8h Etoposide treated

label_protocol: Illumina® TotalPrep™-96 RNA Amplification Kit

growth_protocol: HEK293 p65wt and p65S547A were cultured in DMEM supplemented with 10% FBS, 1% L-glu, and 1% Penicillin/Streptavidine

extract_protocol: Standard protocol of the Rneasy Mini Kit (Qiagen)

treatment_protocol: Cells were either left untreated or treated with Etoposide for 4 or 8 hours

tag: lentiviral transduction

value: siRNA resistant HA-p65S547A

tag: transfection

value: p65 siRNA to knock down endogenous p65


title: 293 p65S547A Etop8h repl1

description:
SAMPLE 16
replicate 1


title: LB stationary STM1230


title: LB stationary STM1444


title: LB stationary STM1391


title: LB stationary STM1753


title: LB stationary STM2688


title: LB stationary PSLT041


title: LB stationary STM0982


title: LB stationary STM2640


title: LB stationary STM0118


title: MHCC97-H CD44s shRNA (7165895058_A)

description: Replicate 2


title: 293 p65wt Etop8h repl3

description:
SAMPLE 9
replicate 3

source_name: HEK293 p65 wt 8h Etoposide treated

value: siRNA resistant HA-p65wt


title: 293 p65S547A ctrl repl3

description:
SAMPLE 12
replicate 3

source_name: HEK293 p65S547A non-treated


title: 293 p65S547A Etop4h repl3

description:
SAMPLE 15
replicate 3

source_name: HEK293 p65S547A 4h Etoposide treated


title: 293 p65S547A Etop4h repl2

description:
SAMPLE 14
replicate 2


title: 293 p65S547A ctrl repl2

description:
SAMPLE 11
replicate 2


title: 293 p65S547A Etop8h repl2

description:
SAMPLE 17
replicate 2


title: 293 p65S547A Etop4h repl1

description:
SAMPLE 13
replicate 1


title: LB log STM4361

source_name: LB log phase 3 h

source_name: LB stationary phase 18 h


title: 293 p65S547A ctrl repl1

description:
SAMPLE 10
replicate 1


title: LB log STM3466


title: LB log STM3501


title: 293 p65wt Etop8h repl2

description:
SAMPLE 8
replicate 2


title: LB log STM2826


title: 293 p65wt Etop8h repl1

description:
SAMPLE 7
replicate 1


title: LB log STM2688


title: 293 p65wt Etop4h repl3

description:
SAMPLE 6
replicate 3

source_name: HEK293 p65 wt 4h Etoposide treated


title: 293 p65wt Etop4h repl2

description:
SAMPLE 5
replicate 2


title: 293 p65wt ctrl repl3

description:
SAMPLE 3
replicate 3

source_name: HEK293 p65 wt non-treated


title: 293 p65wt Etop4h repl1

description:
SAMPLE 4
replicate 1


title: LB log STM2924


title: LB log STM2640


title: LB log STM1753


title: 293 p65wt ctrl repl1

description:
SAMPLE 1
replicate 1


title: LB log STM0982


title: LB log STM1391


title: LB log STM0118


title: LB log STM1230


title: LB log PSLT041


title: 293 p65wt ctrl repl2

description:
SAMPLE 2
replicate 2


title: LB log STM1444


title: Liver_Lactation_replicate4

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

country: Germany

institute: JLU Gießen

hyb_protocol: After checking the quality and quantity of the labeled cRNA, cRNA was fractionated and hybridized with the Affymetrix GeneChips. GeneChips were washed and stained with the Affymetrix GeneChip Fluidics station 450. The GeneChips were then scanned with an Affymetrix GeneChip scanner 3000. All procedures were performed according to Affymetrix protocols (GeneChip expression analysis, Technical manual from Affymetrix). The quality of hybridization was assessed in all samples following the manufacturer´s recommendations.

scan_protocol: After scanning the arrays, cell intensity files containing a single intensity value for each probe cell were computed from the image data with the Affymetrix GeneChip Command Console Software.

data_processing: Probe cell intensity data were further analyzed in the Affymetrix Expression Console software using the Robust Multichip Analysis (RMA) algorithm.

label: Biotin

organism: Sus scrofa

label_protocol: The cRNA was labeled with biotin using the Affymetrix GeneChip labeling kit.

extract_protocol: Total RNA from frozen liver samples was isolated using TrizolTM reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer´s protocol and purified using the RNeasy Minikit (Qiagen, Hilden, Germany).

value: female

tag: condition

value: lactating

tag: tissue

value: Liver


title: Liver_Lactation_replicate1


title: Liver_Lactation_replicate2


title: Liver_control_replicate4

value: control


title: Liver_control_replicate1


title: S.cerevisiaeTN2080_SC-ura_8h

city: Hiroshima

first: Kozo

last: Ochi

state: Hiroshima

address: 2-1-1 Miyake, Saeki-ku

department: Food Sciences and Biotechnology

country: Japan

institute: Hiroshima Institute of Technology

description: This sample is of S.cerevisiae INVSc1 harboring the  pTN1035 plasmid(pYC2/CT containing Sj-RSH)

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Arrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices).

data_processing: Gene expression levels were calculated with NimbleScan software version 2.3 (Roche NimbleGen) using the median polish normalization method and relative signal intensities were generated using the robust multi-array average algorithm.

organism: Saccharomyces cerevisiae

source_name: Strain TN2080 is INVSc1 transformed with pTN1035. pTN1035 is pTN1034 with Sj-RSH deleting 5' unttranslated region.

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
Saccharomyces cerevisiae strain TN2080 (accumulating ppGpp) was grown to mid-growth phase (8 h) in SC-uracil medium containing 2% galactose (to express Sj-RSH) at 30℃ ( Sherman, F. Methods in Enzymology 194, 3-21 (1991)).
Saccharomyces cerevisiae strain TN2077 (vector contorol) was grown to mid-growth phase (8 h) in SC-uracil medium containing 2% galactose (to express Sj-RSH)  at 30℃ (Sherman, F. Methods in Enzymology 194, 3-21 (1991)).

extract_protocol: Total RNA was extracted using Isogen-LS reagent (Nippon Gene) with chloroform, and purification was done following the manufacture's instructions. Purification was further performed using RNeasy Kit with RNase free DNase I (Qiagen GmbH, Germany). Concentration of purified RNA was determined spectroscopically at 260 nm.

treatment_protocol: S.cerevisiae cells grown for 8 h were placed into 50ml tubes with cyclohexamide (final concn. 10 µg/ml), and then centifuged at 3,000 × g for 5 min at 4℃. Cell pellets were frozen and kept at -80℃ until use for RNA extraction.

tag: plasmid

value: SjRSH expression plasmid


title: Liver_control_replicate2


title: Liver_Lactation_replicate3


title: S.cerevisiaeTN2077_SC-ura_8h

description: This sample is of S.cerevisiae INVSc1 harboring the pYC2/CT vector(control)

source_name: Strain TN2077 is INVSc1(Invitrogen) transformed with pYC2/CT(Invitrogen)

value: vector


title: healthy_02

city: Heidelberg

first: Constance

middle: Regina

last: Baer

address: Im Neuenheimer Feld 280

department: Epigenomics and Cancer Risk Factors

institute: German Cancer Research Center

description: MCIp enrichment according to Gebhard et al. 2006

hyb_protocol: Human Cot-1 DNA (blocking), formamid and hybridization components (Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit) were added according to the manufacturer's recommendations (Human CpG Island Microarray protocol), samples were applied to microarrays enclosed in Agilent G2534A Microarray Hybridization chambers and incubated at 67°C for 48 hrs in a rotating hybridization oven (20 rpm). After hybridization, slides were washed (washing buffers 1 and 2 [Agilent] and acetonitrile) according to the manufacturer's (Human CpG Island Microarray protocol).

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.10.5.1.1). Agilent G2565BA Microarray Scanner

data_processing: Agilent Feature Extraction Software (v 10.5.1.1), Protocol: ChIP_105_Dec08. Background-correction: normal-exponential convolution method with offset 50 (Silver et al. 2009); within-array normalization: rank-invariant weighted loess regression (Tseng et al. 2001) using the statistical environment R v2.11, package RJaCGH v2 and the Bioconductor suite.

source_name: MCIp enriched, healthy donor CD19 sorted B cells of the peripheral blood

label_protocol: DNA was labelled with BioPrime Total Genomic Labeling System (Invitrogen) according to the manufacturer's recommendations.

extract_protocol: DNA isolation: Qiagen DNeasy; purification after MCIp enrichment: MinElute PCR Purification Kit (Qiagen) according to manufacturers instruction

tag: tissue origin

value: peripheral blood

tag: origin

value: primary cells

source_name: MCIp enriched, pool of CD19 sorted B cells of the peripheral blood from healthy donors

value: pool of 5 males and 5 females


title: Liver_control_replicate3


title: healthy_01

value: male


title: CLL_24

source_name: MCIp enriched, CLL patient CD19 sorted B cells of the peripheral blood


title: s/nsMyc-LCOs DMI3 6h roots biological replicate 1

city: Hannover

first: Helge

last: Küster

address: Herrenhäuser Str. 2

department: Institut für Pflanzengenetik

institute: Leibniz Universität Hannover

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

hyb_protocol: 12.5 ug of fragmented aRNA was added to a 250 ul cocktail also containing hybridization controls. 200 ul of the mixture was hybridized on GeneChips for 16 h at 45C. Standard post hybridization wash and double-stain protocols (FS450_0001; GeneChip HWS kit; Affymetrix, Santa Clara, CA, USA) were used on an Affymetrix GeneChip Fluidics Station 450.

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

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

label: biotin

organism: Medicago truncatula

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

growth_protocol: Medicago truncatula Gaertn cv Jemalong NFP and DMI3 seeds were surface-sterilized and scarified. Plates with M. truncatula seeds were incubated for 24 hours in the climate chamber (humidity: 70 %; photosynthetic photon flux: 150 μmol m-2 s-1) at a 16 h light (23 °C) and 8 h dark (18 °C) regime. Subsequently, seedlings were moisturized with sterile water (pH 7.0) to allow careful removal of seed coats. In each case, eight seedlings were put on the upper quarter of a 2.5 % (w/v) phytoagar (Duchefa Biochemie, Haarlem, The Netherlands) slant plate (120 x 120 mm; DoctorLab, Jena, Germany). Seedlings used for treatment with Myc-LCOs and corresponding controls were put on plates with half-strength Hoagland´s solution (Arnon and Hoagland, 1940) set to pH 6.5 with KOH. An approximately one cm strap of Whatman paper (Schleicher & Schuell, Dassel, Germany) soaked with appropriate nutrient solutions as described above was used to fix the seedlings on the plates beneath the cotyledons. Three plates at a time were sealed with transparent wrapping foil, which was cut at the upper side to allow gas exchange. The lower half of each plate stack was wrapped with aluminium foil for light protection to allow normal root development. Each triple pack of plates was placed in an approximately 70° angle in the climate chamber for five days.

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

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

tag: treatment

value: s/nsMyc-LCOs

tag: time

value: Root

tag: genetic background

value: Jemalong A17

tag: genotype

value: DMI3 mutant

value: 10 days


title: CLL_23


title: DMI3 control 6h roots biological replicate 3

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

tag: age


title: s/nsMyc-LCOs DMI3 6h roots biological replicate 3

source_name: Medicago truncatula DMI3 plantlet roots treated with Myc LCOs


title: s/nsMyc-LCOs DMI3 6h roots biological replicate 2


title: CLL_21


title: CLL_20


title: CLL_19


title: DMI3 control 6h roots biological replicate 2

source_name: Medicago truncatula DMI3 plantlet roots treated with control solution


title: DMI3 control 6h roots biological replicate 1


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

value: nsMyc-LCOs


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


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


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

value: sMyc-LCOs


title: CLL_22


title: CLL_15


title: CLL_17

value: female


title: CLL_16


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

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

value: NFP mutant


title: NFP control 6h roots biological replicate 3

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


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


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


title: NFP control 6h roots biological replicate 2

source_name: Medicago truncatula NFP plantlet roots treated with control solution


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

source_name: Medicago truncatula NFP plantlet roots treated with Myc LCOs


title: NFP control 6h roots biological replicate 1


title: CLL_13


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


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


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


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


title: CLL_14


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


title: CLL_12


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


title: CLL_11


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


title: CLL_10


title: Nod-LCO control 24h roots biological replicate 2

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

growth_protocol: Medicago truncatula Gaertn cv Jemalong genotype A17 seeds were surface-sterilized and scarified. Plates with M. truncatula seeds were incubated for 24 hours in the climate chamber (humidity: 70 %; photosynthetic photon flux: 150 μmol m-2 s-1) at a 16 h light (23 °C) and 8 h dark (18 °C) regime. Subsequently, seedlings were moisturized with sterile water (pH 7.0) to allow careful removal of seed coats. In each case, eight seedlings were put on the upper quarter of a 2.5 % (w/v) phytoagar (Duchefa Biochemie, Haarlem, The Netherlands) slant plate (120 x 120 mm; DoctorLab, Jena, Germany). Seedlings used for treatment with Myc-LCOs and corresponding controls were put on plates with half-strength Hoagland´s solution (Arnon and Hoagland, 1940) set to pH 6.5 with KOH, whereas seedlings treated with Nod-LCOs and corresponding controls were grown on slant agar plates with an N-free nutrient solution of pH 7.5 as described in Baier et al. (2007), further on referred to as NH-mix. An approximately one cm strap of Whatman paper (Schleicher & Schuell, Dassel, Germany) soaked with appropriate nutrient solutions as described above was used to fix the seedlings on the plates beneath the cotyledons. Three plates at a time were sealed with transparent wrapping foil, which was cut at the upper side to allow gas exchange. The lower half of each plate stack was wrapped with aluminium foil for light protection to allow normal root development (Figure 1 E). Each triple pack of plates was placed in an approximately 70° angle in the climate chamber for five days.

treatment_protocol: Plantlets were carefully removed from slant agar plates and placed in 13 mL tubes wrapped with aluminium foil that were cut off at the 8 mL mark, using 20 plantlets per tube (Sarstedt, Nürnbrecht, Germany). Each tube contained 5 mL of the following solutions: sulphated Myc-LCO solution (half-strength Hoagland´s solution of pH 6.5 containing 10-8 M sulphated Myc-LCOs), non-sulphated Myc-LCO solution (half-strength Hoagland´s solution of pH 6.5 containing 10-7 M non-sulphated Myc-LCOs), mixed sulphated and non-sulphated Myc-LCO solution (half-strength Hoagland´s solution of pH 6.5 containing 10-8 M sulphated and 10-7 M non-sulphated Myc-LCOs), Myc control solution (half-strength Hoagland´s solution of pH 6.5), Nod-LCO solution (NH-mix of pH 7.5 containing 10-8 M Nod-LCOs), and Nod control solution (NH-mix of pH 7.5). After 6 h of incubation in the climate chamber, 10 plantlets per batch were removed from the treatment or control solutions and harvested, while the other 10 remained in the respective solutions for a total of 24 h.


title: Nod-LCO control 24h roots biological replicate 3

source_name: Medicago truncatula plantlet roots treated with control solution


title: Myc-LCOs control 24h roots biological replicate 3


title: Myc-LCOs control 6h roots biological replicate 2


title: CLL_08


title: Nod-LCO control 24h roots biological replicate 1


title: Myc-LCOs control 24h roots biological replicate 1


title: Myc-LCOs control 6h roots biological replicate 3


title: CLL_04


title: Nod-LCOs 24h roots biological replicate 2

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

value: Nod-LCOs


title: Nod-LCOs 24h roots biological replicate 1

source_name: Medicago truncatula plantlet roots treated with symbiotic LCOs


title: Nod-LCOs 24h roots biological replicate 3


title: Myc-LCOs control 6h roots biological replicate 1

value: control


title: Myc-LCOs control 24h roots biological replicate 2


title: CLL_09


title: s/nsMyc-LCOs 24h roots biological replicate 3


title: CLL_03


title: CLL_06


title: CLL_01


title: CLL_02


title: CLL_07


title: s/nsMyc-LCOs 24h roots biological replicate 2


title: CLL_05


title: s/nsMyc-LCOs 24h roots biological replicate 1


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


title: HCT-116_DKO

hyb_protocol: Human Cot-1 DNA (blocking) and hybridization components (Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit) were added according to the manufacturer's recommendations (ChIP-on-Chip protocol), samples were applied to microarrays enclosed in Agilent G2534A Microarray Hybridization chambers and incubated at 65°C for 48 hrs in a rotating hybridization oven (20 rpm). After hybridization, slides were washed (washing buffers 1 and 2 [Agilent] and acetonitrile) according to the manufacturer's (ChIP-on-Chip protocol).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1), Protocol: ChIP_105_Dec08. Analysis of H3K4me3 ChIP data was performed with the CoCAS ChIP-on-chip analysis suite (Benoukraf et al. 2009) using rotation by principal components analysis and weighted loess on the first-order differences of neighbouring probes for normalization (Peng et al. 2007) and a binding ratio threshold for peak detection.

source_name: H3K4me3 enriched, HCT-116, colorectal carcinoma cell line, DNMT1/3b knock out

label_protocol: isolated DNA was labelled with BioPrime® Total Genomic Labeling System (Invitrogen) according to the manufacturer's recommendations

growth_protocol: cell lines were grown under standard conditions, primary cells were not cultured

extract_protocol: chromatin IP (ChIP) was performed with H3K4me3 antibody according to standard protocols (Diagenode ChIP kit), DNA was extracted with magnetic beads (Diagenode IPure kit)

treatment_protocol: DAC treatment was performed in 24 h intervals for 168 hrs (192 hrs for Granta-519), DAC concentration was 200 nm for Kasumi-1 and 1500 nM for Granta-519, MEC-1 and EHEB

tag: cell line

tag: antibody

value: cell line

tag: lineage

value: colon epithelium

tag: genotype/variation

value: DNMT1/3b knock out


title: CLL_18

tag: gender

value: peripheral blood

value: primary cells


title: HCT-116_WT

source_name: H3K4me3 enriched, HCT-116, colorectal carcinoma cell line, wild type

value: wild type


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

value: s/nsMyc-LCOs


title: 193-00

city: Minneapolis

first: Anthony

middle: James

last: Smith

state: MN

address: 420 Delaware Street S.E.

department: Microbiology

institute: University of Minnesota

description: cervix

hyb_protocol: All RNA samples (15 micrograms of each fragmented cRNA) were hybridized to Affymetrix GeneChip Rhesus Macaque Genome Arrays (Santa Clara, CA).  After hybridization, chips were washed, stained with streptavidin-PE, and scanned with GeneChip Operating Software at the Biomedical Genomics Center at the University of Minnesota. The experiments from each RNA sample were duplicated in the preparation of each cRNA probe and microarray hybridization.

scan_protocol: Scanned with GeneChip Operating Software at the Biomedical Genomics Center at the University of Minnesota.

data_processing: The R package “affy” was used to generate robust multi-chip average (RMA) values for all arrays based on the CEL files produced by the Affymetrix data analysis platform.  Some samples had multiple arrays, hence the mean RMA values for those samples were computed and used in the subsequent analysis. The RMA algorithm produces a summary of gene expression that is of log scale; we used this log scale for all subsequent analyses.  To test for differences across groups, weighted least squares with an effect for group was used (weights were used because some RMA values were the mean of multiple measurements).  The resulting p-values were converted to q-values using the q-vale package in R in order to look for genes of interest.  Genes were selected based on their associated q-values (< 0.2) and fold change in expression (> 1.2).

organism: Macaca mulatta

source_name: Cervix from SIVmac239-∆Nef-vaccinated Rhesus macaque challenged intravaginally with SIVmac251 (4-5 days post exposure)

label_protocol: Double stranded cDNA and biotin-labeled cRNA probes were synthesized from 5 micrograms of total RNA with a MessageAmp II aRNA kit (Ambion). The cRNA probes were column purified and fragmented with a Fragmentation kit (Ambion).

extract_protocol: Frozen cervical specimens were homogenized with a power homogenizer (Heat Systems Ultrasonic) in TRIzol (Invitrogen) without thawing.  Total RNA was isolated following the manufacturer’s protocol and further purified with an RNeasy Mini Kit (Qiagen).

treatment_protocol: Cervix was removed from 17 Rhesus macaques (3 uninfected animals; 5 unvaccinated animals 4-5 days post vaginal exposure with SIVmac251; 4 SIVmac239-∆Nef-vaccinated animals before challenge; 5 SIVmac239-∆Nef-vaccinated animals 4-5 days post vaginal exposure with SIVmac251) housed at the New England Primate Center in accordance with the regulations of the American Association of Accreditation of Laboratory Animal Care and the standards of the Association for Assessment and Accreditation of Laboratory Animal Care International.  At the time of euthanasia, the relevant region of cervix was dissected away from most of the uterus and vagina and then further divided into four quadrants.  Tissue pieces from each quadrant were either snap-frozen, fixed in 4% paraformaldehyde or SafeFix II and embedded in paraffin for later sectioning, or used unfixed for other assays.

value: Cervix

value: Female


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

value: Root

value: Jemalong A17


title: nsMyc-LCOs 24h roots biological replicate 3

value: nsMyc-LCOs

value: 10 days


title: nsMyc-LCOs 6h roots biological replicate 1


title: EHEB_DAC

source_name: H3K4me3 enriched, EHEB, lymphoid cell line derived from CLL, 1500 nm DAC for 168 hrs

value: EHEB

value: lymphoid

value: 1500 nm DAC for 168 hrs


title: HL-60

source_name: H3K4me3 enriched, HL-60, myeloid cell line

value: myeloid

source_name: HL-60, myeloid cell line


title: JURKAT

source_name: H3K4me3 enriched, JURKAT, T lymphocytic cell line

value: JURKAT

value: cell line

source_name: JURKAT, T lymphocytic cell line


title: 143-09

description: cervix


title: nsMyc-LCOs 24h roots biological replicate 1


title: nsMyc-LCOs 6h roots biological replicate 3


title: 142-09

description: cervix, biological replicates 1-2

source_name: Cervix from SIVmac239-∆Nef-vaccinated Rhesus macaque (140 days post vaccination)


title: 174-96

description: cervix, biological replicates 1-2


title: sMyc-LCOs 24h roots biological replicate 3

value: sMyc-LCOs


title: 528-00

description: cervix


title: Mec-1_untreated

source_name: H3K4me3 enriched, MEC-1, lymphoid cell line derived from PLL, untreated


title: nsMyc-LCOs 24h roots biological replicate 2


title: EHEB_untreated

source_name: H3K4me3 enriched, EHEB, lymphoid cell line derived from PLL, untreated


title: 135-09

description: cervix


title: sMyc-LCOs 24h roots biological replicate 2


title: 139-09

description: cervix


title: 140-09

description: cervix, biological replicates 1-2


title: sMyc-LCOs 24h roots biological replicate 1


title: healthy_04

source_name: H3K4me3 enriched, healthy donor CD19 sorted B cells of the peripheral blood

tag: cell type

value: CD19 sorted B cells


title: healthy_03

value: primary cells

source_name: healthy donor CD19 sorted B cells of the peripheral blood


title: nsMyc-LCOs 6h roots biological replicate 2


title: Mec-1_DAC

source_name: H3K4me3 enriched, MEC-1, lymphoid cell line derived from PLL, 1500 nm DAC for 168 hrs


title: CLL_26

source_name: H3K4me3 enriched, CLL patient CD19 sorted B cells, male

source_name: CLL patient CD19 sorted B cells, male


title: sMyc-LCOs 6h roots biological replicate 2

source_name: Medicago truncatula plantlet roots treated with symbiotic LCOs


title: Granta-519_untreated

source_name: H3K4me3 enriched, Granta-519, lymphoid cell line derived from MCL, untreated


title: 32109

description: cervix

source_name: Cervix from Rhesus macaque infected intravaginally with SIVmac251 (4-5 days post exposure)


title: Kasumi-1_DAC

source_name: H3K4me3 enriched, Kasumi-1, myeloid cell line, 200 nm DAC for 168hrs

value: 200 nm DAC for 168hrs


title: sMyc-LCOs 6h roots biological replicate 3


title: 2823_Female_750ppm_Postnatal

city: Philadelphia

first: Keyur

last: Talsania

address: 1020 Locust St

department: Pathology

institute: Thomas Jefferson University

description: Gene expression in hippocampus at Postnatal developmental period and at 750ppm lead exposure level

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr on Rat Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Raw gene expression data was normalized using RMA in Partek Genomics Suit.

organism: Rattus norvegicus

source_name: Hippocampus

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA.

extract_protocol: Tissue was extracted using Qiagen miRNeasy kits according to the manufacturers protocol on a Qiagen Qiacube Automated Extraction system.  Following extraction samples underwent QA/QC checks using a GE NanoVue Spectrophotometer and were then run on an Agilent Bioanalyzer 2100 for RNA integerity.

treatment_protocol: Animals received either perinatal or postnatal exposure to control chow, control chow containing 250ppm lead-acetate or control chow containing 750ppm lead acetate.  Perinatal exposure consisted of the dams being placed on lead food for 10 days pior to breeding and remaining on this food until weening, at which time the weaned pups were placed on control food until the end of the experiment at PND55.  Postnatal animals only received lead-containgin food from brith through to PND 45, then were placed on control food until PND 55. Animals were euthanized and hippocampii immediately dissected and flash frozen.  Samples were then stored at -80 degrees C until processed.

tag: developmental period

value: Postnatal

tag: lead exposure level


title: 28018

description: cervix

tag: tissue

value: Cervix


title: 138-09

description: cervix, biological replicates 1-2

value: Female


title: 31098

description: cervix


title: Kasumi-1_untreated

source_name: H3K4me3 enriched, Kasumi-1, myeloid cell line, untreated

source_name: Kasumi-1, myeloid cell line, untreated


title: INCB18424 Persistent 1

city: New York

first: Ross

last: Levine

state: NY

department: Human Oncology & Pathogenesis Program

institute: Memorial Sloan-Kettering Cancer Center

description: SAMPLE 7

hyb_protocol: Please see Affymetrix Expression Analysis Technical Manual, with Specific Protocols for Use with the Hybridization, Wash, and Stain Kit (http://www.affymetrix.com/estore/browse/products.jsp?categoryIdClicked=&productId=131415#1_3)

scan_protocol: Please see AffymetrixExpression Analysis Technical Manual, with Specific Protocols for Use with the Hybridization, Wash, and Stain Kit (http://www.affymetrix.com/estore/browse/products.jsp?categoryIdClicked=&productId=131415#1_3)

data_processing: Partek GS (v.6.5): GCRMA Background Correction : Quantile Normalization : Log2 transform : Median Polish

organism: Mus musculus

source_name: BaF3 cell line transduced MPLW515L3 mutant grown in 0.8 uM INCB18424 for 4 wks

label_protocol: Please see Affymetrix 3' IVT Express Kit Documentaion (http://www.affymetrix.com/estore/browse/products.jsp?categoryIdClicked=&productId=131415#1_3)

growth_protocol: Cells cultured in RPMI 10% FCS

extract_protocol: Total RNA extracted using Trizol according to manufacturer's guidelines

treatment_protocol: Either 1) Naïve cells treated with DMSO for 4 hours 2) Naïve cells treated with 0.8 uM INCB18424 for 4 hours or 3) Persistent cells treated with 0.8 uM INCB18424 for 4 hours

tag: infected with

tag: pretreated with

value: 0.8 uM INCB18424 for 4 wks (Persistent)

tag: treated with

value: 0.8 uM INCB18424 for 4 hrs

tag: sample type

value: persistent


title: INCB18424 Persistent 2

description: SAMPLE 8


title: CLL_25

source_name: H3K4me3 enriched, CLL patient CD19 sorted B cells of the peripheral blood, male

tag: origin


title: INCB18424 Acute 2

description: SAMPLE 5

source_name: BaF3 cell line transduced MPLW515L3 mutant

value: normal condition (Naïve)

value: acute


title: implantation sites from control uteri

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

country: Spain

institute: Universidad de Zaragoza

description: Gene expression data from control and implanted uterine sites

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip

scan_protocol: GeneChips were scanned using the GeneArray Scanner (Agilent Technologies, Palo Alto, CA, USA

data_processing: The data were analyzed with Affymetrix GCOS 1.4 using Affymetrix default analysis settings and global scaling as normalization method

source_name: Uterus RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 microg total RNA

growth_protocol: four- month-old females were used

extract_protocol: Tri reagent extraction of total RNA was performed according to the manufacturer's instructions. RNA was extracted using a Quiagen RNeasy kit

treatment_protocol: Implantation sites were dissected out the uterus.

tag: genetic background

value: C57Bl/6J X OLA129

value: female

tag: pregnancy

value: eight day

value: 4 months

value: uterus implantation site

value: control


title: interimplantation sites from Cbs-deficient uteri

description: Gene expression data from Cbs-deficient and interimplantation uterine sites

source_name: Interimplantation Uterus RNA

treatment_protocol: Interimplantation sites were dissected from the uterus.

tag: age

value: uterus inter-implantation site

tag: genotype

value: Cbs null


title: 2824_Female_750ppm_Postnatal


title: INCB18424 Acute 1

description: SAMPLE 4

tag: cell line


title: 34572

description: cervix, biological replicates 1-3

source_name: Cervix from uninfected Rhesus macaque


title: implantation sites from Cbs-deficient uteri

description: Gene expression data from Cbs-deficient mice and implanted uterine sites


title: Granta-519_DAC

source_name: H3K4me3 enriched, Granta-519, lymphoid cell line derived from MCL, 1500 nm DAC for 192 hrs

tag: antibody

value: cell line

tag: lineage

value: lymphoid

tag: treatment

value: 1500 nm DAC for 192 hrs


title: sMyc-LCOs 6h roots biological replicate 1

tag: time

value: sMyc-LCOs

value: Root

value: Jemalong A17

value: 10 days


title: INCB18424 Acute 3

description: SAMPLE 6

value: normal condition (Naïve)

value: 0.8 uM INCB18424 for 4 hrs


title: 31917

description: cervix, biological replicates 1-2

value: Cervix

tag: gender

value: Female


title: 31373

description: cervix


title: 34550

description: cervix, biological replicates 1-2


title: HUVEC_siPML-2_rep2

city: Cleveland

first: Hung-Ying

last: Kao

state: OH

address: 2123 Adelbert Road, RT400-L

department: Biochemistry

institute: Case Western Reserve University

description: HUVEC cells with passage number less than 5 were transfected with PML siRNA number 2 for 72 hrs before total RNA extraction. This is one of the technical replicates loaded on microarray chip B.

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 1.14.0). It was vst transformed and rsn normalized.

source_name: HUVEC cells, passage number less than 5, siPML-2 transfected for 72hrs, technical replicate 2

label_protocol: standard as recommended by illumina

extract_protocol: The total RNA was extracted with the PrepEase RNA spin Kit (USB cat#:78766 1 KT) following the manufacturer's instructions.

value: HUVEC cells

tag: cell passage

value: less than 5

tag: sirna

value: siPML-2 transfected for 72hrs


title: INCB18424 Persistent 3

description: SAMPLE 9

tag: infected with

value: 0.8 uM INCB18424 for 4 wks (Persistent)

value: persistent


title: interimplantation sites from control uteri

description: Gene expression data from control and interimplantation uterine sites

source_name: Interimplantation sites Uterus

value: C57Bl/6J X OLA129

value: female

value: eight day

value: 4 months

tag: tissue

value: uterus inter-implantation site

value: control


title: 31427

description: cervix


title: 2822_Female_750ppm_Postnatal

tag: developmental period

value: Postnatal

tag: lead exposure level


title: 02 220-8 STI 12-hrs

city: BERKELEY

first: Patty

middle: B

last: Garcia

state: CA

address: 439 LSA

institute: UC BERKELEY

description: AMuLV pro-B cell lines STI-treated and quantified for miRNA expression

hyb_protocol: done by Exiqon

scan_protocol: done by Exiqon

data_processing: Data processing was performed by Exiqon according to manufacturer protocol; in brief normalization means background subtraction and normalization with a global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. This within-slide normalization is performed to minimize differences between the colours in an intensity-dependent manner. The criteria for deciding that the calling of a miRNA had failed on a particular array, was that 2 or more of the 4 replicated measures of this miRNA were flagged 1 or 2 (i.e. the signal is below background) by the image analysis software. Further in the expression matrix all capture probes with Cy3 and Cy5 signals lower than 1.5x of the median signal intensity of the given slide were excluded. Replicated measurements of the same miRNA from each slide were averaged to per-chip median values and then used to obtain geometric means and standard deviations for each miRNA.

source_name: STI-treated

label_protocol: done by Exiqon

growth_protocol: cell lines were grown in RPMI supplemented with 5%FCS

extract_protocol: Qiagen miRNeasy kit

treatment_protocol: cels were treated for 12 hours with STI571 at 2.5uM to induce change in miRNA expression profile.

value: Abelson B

tag: cell type

value: AMuLV pro-B

source_name: reference pool (2ug RNA from each of the sample)


title: 05 63-12 untreated

description: AMuLV pro-B cell lines untreated and quantified for miRNA expression

source_name: Untreated


title: 04 E47+/+ STI 12-hrs


title: 06 63-12 STI 12-hrs


title: 03 E47+/+ untreated


title: 2821_Female_750ppm_Postnatal


title: HUVEC_siPML-2_rep1

description: HUVEC cells with passage number less than 5 were transfected with PML siRNA number 2 for 72 hrs before total RNA extraction. This is one of the technical replicates loaded on microarray chip A.

source_name: HUVEC cells, passage number less than 5, siPML-2 transfected for 72hrs, technical replicate 1


title: HUVEC_siCtrl_rep2

description: HUVEC cells with passage number less than 5 were transfected with non-targeting control siRNA for 72 hrs before total RNA extraction. This is one of the technical replicates located on microarray chip B.

source_name: HUVEC cells, passage number less than 5, siCtrl transfected for 72hrs, technical replicate 2

value: siCtrl transfected for 72hrs


title: DMSO Control 3

description: SAMPLE 3

tag: pretreated with

value: normal condition (Naïve)

tag: treated with

value: DMSO for 4 hrs

tag: sample type


title: 01 220-8 untreated


title: 2843_Female_250ppm_Postnatal

description: Gene expression in hippocampus at Postnatal developmental period and at 250ppm lead exposure level

source_name: Hippocampus

value: Female


title: 2842_Female_250ppm_Postnatal


title: 1981_Female_750ppm_Perinatal

description: Gene expression in hippocampus at Perinatal developmental period and at 750ppm lead exposure level

value: Perinatal


title: 2844_Female_250ppm_Postnatal


title: DMSO Control 2

description: SAMPLE 2


title: 1980_Female_750ppm_Perinatal


title: HUVEC_siPML-1_rep1

description: HUVEC cells with passage number less than 5 were transfected with PML siRNA number 1 for 72 hrs before total RNA extraction. This is one of the technical replicates loaded on microarray chip A.

source_name: HUVEC cells, passage number less than 5, siPML-1 transfected for 72hrs, technical replicate 1

value: HUVEC cells

value: less than 5

value: siPML-1 transfected for 72hrs


title: DMSO Control 1

description: SAMPLE 1


title: 1978_Female_750ppm_Perinatal


title: HUVEC_siPML-1_rep2

description: HUVEC cells with passage number less than 5 were transfected with PML siRNA number 1 for 72 hrs before total RNA extraction. This is one of the technical replicates loaded on microarray chip B.

source_name: HUVEC cells, passage number less than 5, siPML-1 transfected for 72hrs, technical replicate 2


title: 1979_Female_750ppm_Perinatal


title: C2C12, dl928 infected, 36h, biological replicate 2, technical replicate B

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

description: gene expression data from C2C12 cells after 36h post infection

hyb_protocol: cRNA were hybridized following standard Affymetrix protocol (GeneChip Expression Analysis Tachnical manual, 701021 rev. 4). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix® GeneChip® Scanner   3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. Alpha1:  0.05; Alpha2:  0.065; Tau:  0.015.

source_name: C2C12, YH47 infected, 36h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip Expression Analysis Tachnical manual, 701021 rev. 4) from 5 ug total RNA.

growth_protocol: C2C12 myoblasts, cultured in collagen-coated dishes in DMEM with 10% FBS, were induced to differentiate by serum deprivation for 72 hours in the presence of 50 mM 1-D-arabinofuranosylcytosine.

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

treatment_protocol: Mutant or recombinant adenoviruses used for infections were as follows: dl520, expressing the 12S form of E1A; YH47/dl928, expressing the 12S form of a mutated E1A protein (Y47H, and C124G); and dl312, bearing a deletion of essentially the entire E1A gene. Recombinant Ad-E2F1 and Ad-CRE expressed their respective cDNAs under CMV promoter. A MOI of 300 was used in all cases.

value: myotubes

value: dl928 infected


title: 2841_Female_250ppm_Postnatal


title: HUVEC_siCtrl_rep1

description: HUVEC cells with passage number less than 5 were transfected with non-targeting control siRNA for 72 hrs before total RNA extraction. This is one of the technical replicates located on microarray chip A.

source_name: HUVEC cells, passage number less than 5, siCtrl transfected for 72hrs, technical replicate 1


title: 2860_Female_250ppm_Perinatal

description: Gene expression in hippocampus at Perinatal developmental period and at 250ppm lead exposure level


title: 2859_Female_250ppm_Perinatal


title: 2857_Female_250ppm_Perinatal


title: C2C12, dl928 infected, 24h, biological replicate 1, technical replicate B

description: gene expression data from C2C12 cells after 24h post infection

source_name: C2C12, YH47 infected, 24h


title: C2C12, dl928 infected, 36h, biological replicate 1, technical replicate B


title: C2C12, dl928 infected, 24h, biological replicate 2, technical replicate B


title: C2C12, dl520 infected, 36h, biological replicate 1, technical replicate B

source_name: C2C12, E1A infected, 36h

value: dl520 infected


title: 1975_Female_Control

description: Gene expression in hippocampus

value: Control

value: 0ppm (Control)


title: 1977_Female_Control

description: Gene expression in hippocampus


title: 2847_Male_750ppm_Postnatal

description: Gene expression in hippocampus at Postnatal developmental period and at 750ppm lead exposure level

value: Male


title: 2848_Male_750ppm_Postnatal

value: Postnatal


title: 1976_Female_Control

description: Gene expression in hippocampus


title: 2874_Male_250ppm_Postnatal


title: C2C12, dl520 infected, 24h, biological replicate 2, technical replicate B

source_name: C2C12, E1A infected, 24h


title: 2876_Male_250ppm_Postnatal


title: C2C12, dl928 infected, 24h, biological replicate 1, technical replicate A


title: C2C12, dl928 infected, 36h, biological replicate 1, technical replicate A


title: C2C12, dl312 infected, 24h, biological replicate 1, technical replicate B

source_name: C2C12, control, 24h

value: dl312 infected


title: C2C12, dl312 infected, 36h, biological replicate 1, technical replicate B

source_name: C2C12, control, 36h


title: 2858_Female_250ppm_Perinatal


title: C2C12, dl928 infected, 36h, biological replicate 2, technical replicate A


title: C2C12, dl520 infected, 36h, biological replicate 2, technical replicate B


title: 2873_Male_250ppm_Postnatal


title: C2C12, dl520 infected, 24h, biological replicate 1, technical replicate B


title: 2875_Male_250ppm_Postnatal


title: C2C12, dl312 infected, 36h, biological replicate 2, technical replicate B


title: 1974_Female_Control

description: Gene expression in hippocampus


title: 2845_Male_750ppm_Postnatal


title: C2C12, dl928 infected, 24h, biological replicate 2, technical replicate A


title: C2C12, dl520 infected, 36h, biological replicate 1, technical replicate A


title: 2846_Male_750ppm_Postnatal


title: C2C12, dl312 infected, 24h, biological replicate 2, technical replicate B


title: 3447_Male_750ppm_Perinatal


title: uPA overexpression 3

city: MIAMI

first: YUQI

last: JING

state: FL

address: 1550 NW 10TH AVE PAP105

institute: University of Miami

description: Replicate

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

source_name: 4T1 tumor

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

growth_protocol: 4T1 cells were transduced by lentiviral vector expresing mouse uPA or empty lentiviral vector. 4T1 cells (uPA overexpresing or empty vector)  (10e5 cells) were implanted into the fifth mammary fat pad of 8-10 weeks old female BALB/c mice.

treatment_protocol: At day 7 after 4T1 cell were inoculated, 4T1 tumors were harvested.

tag: strain

value: Balb/c

value: 4T1 tumor

tag: genotype/variation

value: uPA overexpression


title: 3446_Male_750ppm_Perinatal


title: uPA overexpression 2

description: Replicate


title: 2868_Male_250ppm_Perinatal


title: 3445_Male_750ppm_Perinatal


title: uPA overexpression 1

description: Replicate


title: Empty vector 3

description: Replicate

value: Empty vector


title: C2C12, dl520 infected, 24h, biological replicate 2, technical replicate A

tag: cell line


title: C2C12, dl520 infected, 24h, biological replicate 1, technical replicate A


title: C2C12, dl312 infected, 36h, biological replicate 2, technical replicate A


title: Empty vector 2

description: Replicate


title: 2865_Male_250ppm_Perinatal


title: C2C12, dl312 infected, 24h, biological replicate 2, technical replicate A


title: C2C12, dl520 infected, 36h, biological replicate 2, technical replicate A


title: 3444_Male_750ppm_Perinatal


title: N2A scramble rep2

city: Oxford

first: Ana

last: Marques

address: Oxford

country: United Kingdom

institute: University of Oxford

hyb_protocol: Labeled ssDNA was hybridized to Affymetrix Mouse Gene 1.0 ST

scan_protocol: Chips were processed on an Affymetrix GeneChip Fluidics station 450 and Scanner 3000

data_processing: Limma from the bioconductor package was used to identify differentially expressed genes (Benjamini=Hochberg corrected p-vale <0.05) unig probes with variance between contitions was bigger than 0.5

source_name: N2A transfect with control shRNA

label_protocol: Sense ssDNA was fragment and labeled using GeneChip WT Terminal labeling

growth_protocol: N2A were grown under standard conditions

extract_protocol: RNA extracted using RNAeasy kit (QIAGEN) followed by DNAse treatment with DNA-free kit (AMBION). RNA integrity was assessed on a BioAnalyzer

treatment_protocol: 24h before transfection 1X10 5 cells/well were plated in a 6 well cluster culture vessel. Transient transfection of 4 mg of shRNA and scramble control was carried using lipofectamine Plus (Invitrogen)

value: scramble control


title: 2866_Male_250ppm_Perinatal

value: Perinatal


title: N2A scramble rep3


title: C2C12, dl312 infected, 36h, biological replicate 1, technical replicate A


title: 2867_Male_250ppm_Perinatal


title: 1971_Male_Control

description: Gene expression in hippocampus


title: N2A scramble rep1


title: 1970_Male_Control

description: Gene expression in hippocampus


title: N2A Pbcas4 shRNA rep1

source_name: N2A transfect with mouse Pbcas4 specific shRNA

value: Pbcas4 knockdown


title: Empty vector 1

description: Replicate


title: 1972_Male_Control

description: Gene expression in hippocampus


title: N2A Pbcas4 shRNA rep2


title: 1973_Male_Control

description: Gene expression in hippocampus


title: TbPF_Hygromycin_48h

status: Public on May 30 2012

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

institute: McGill University

description: Treatment with 1.13 μg/ml Hygromycin (EC50), harvested after 48h

hyb_protocol: Equal amounts of Cy3/Cy5-labeled cDNA were mixed and hybridized to version 4 of T. brucei microarrays from Pathogen Functional Genomics Resource Center.

scan_protocol: Microarrays were scanned using ScanArray Express (PerkinElmer).

data_processing: The acquired images were quantified using ScanArray Express software with lowess normalization. Probes that were flagged or were not recognized by the software were ignored. The value for each probe was set to the binary logarithm of treated/control (Cy5/Cy3) median signal ratio, and different probes of each gene were averaged.

organism: Trypanosoma brucei

source_name: Procyclic Form, Hygromycin-treated, 48h

label_protocol: 25 μg RNA was incubated with 9 μg oligo(dT) primer (dT[23]VN, where V is a mixture of A, C and G, and N is any nucleotide) at 70 °C for 10 min, and Cy5- or Cy3-labeled cDNA was synthesized using Superscript III Reverse Transcriptase (Invitrogen) in the presence of 10mM DTT, 0.5 mM of each of dATP, dGTP and dTTP, 0.05 mM dCTP, and 0.05 mM of either Cy5-dCTP or Cy3-dCTP as per manufacturer’s instructions. RNA was hydrolyzed by RNase A and RNase H, and cDNA was cleaned up using Qiagen PCR purification kit.

growth_protocol: Wild-type PF T. brucei cell line IsTat 1.7A was grown in SDM-79 medium in 26 °C, while the cell count was kept between 1.0E+7 and 3.0E+7 cells/ml.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen) and was further purified using RNeasy Mini Kit (Qiagen) as per manufacturers’ intsructions. RNA quality was examined using Agilent 2100 Bioanalyzer prior to cDNA preparation.

treatment_protocol: The cells were treated with 1.13 μg/ml Hygromycin (EC50), for a duration of 48h.

value: IsTat 1.7A

tag: life cycle stage

value: Procyclic Form

source_name: Procyclic Form, no treatment, log phase

treatment_protocol: No treatment.


title: TbPF_Imidazole_48h

description: Treatment with 7.8 mM Imidazole (EC50), harvested after 48h

source_name: Procyclic Form, Imidazole-treated, 48h

treatment_protocol: The cells were treated with 7.8 mM Imidazole (EC50), for a duration of 48h.

tag: treatment


title: TbPF_Pentamidine_48h

description: Treatment with 130 nM Pentamidine (EC50), harvested after 48h

source_name: Procyclic Form, Pentamidine-treated, 48h

treatment_protocol: The cells were treated with 130 nM Pentamidine (EC50), for a duration of 48h.


title: TbPF_NaOH_48h

description: Treatment with 12.5 mM NaOH (EC50), harvested after 48h

source_name: Procyclic Form, NaOH-treated, 48h

treatment_protocol: The cells were treated with 12.5 mM NaOH (EC50), for a duration of 48h.


title: TbPF_Triton-X_48h

description: Treatment with 0.00025% (v/v) Triton-X (EC50), harvested after 48h

source_name: Procyclic Form, Triton-X-treated, 48h

treatment_protocol: The cells were treated with 0.00025% (v/v) Triton-X (EC50), for a duration of 48h.


title: TbPF_Phleomycin_48h

description: Treatment with 31 ng/ml Phleomycin (EC50), harvested after 48h

source_name: Procyclic Form, Phleomycin-treated, 48h

treatment_protocol: The cells were treated with 31 ng/ml Phleomycin (EC50), for a duration of 48h.


title: TbPF_Verapamil_48h

description: Treatment with 1.9 μM Verapamil (EC50), harvested after 48h

source_name: Procyclic Form, Verapamil-treated, 48h

treatment_protocol: The cells were treated with 1.9 μM Verapamil (EC50), for a duration of 48h.


title: TbPF_EtBr_48h

description: Treatment with 2.65 μg/ml EtBr (EC50), harvested after 48h

source_name: Procyclic Form, EtBr-treated, 48h

treatment_protocol: The cells were treated with 2.65 μg/ml EtBr (EC50), for a duration of 48h.


title: TbPF_G418_48h

description: Treatment with 1.13 μg/ml G418 (EC50), harvested after 48h

source_name: Procyclic Form, G418-treated, 48h

treatment_protocol: The cells were treated with 1.13 μg/ml G418 (EC50), for a duration of 48h.


title: IL10-1 6 2008 high pmt

city: Portici (NA)

first: Antonio

last: Di Matteo

address: Via Universita' 100 - Parco Gussone - Edificio 75

department: DiSSPAPA

institute: University of Naples Federico II

description: IL10-1_6 high

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C.  5 ug of Labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20' at 95 °C  Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS).  Hybridization washings were performed as following:  - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20).  - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20).  - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).  - wash with PBST was solution (2X PBS, 0.1% Tween-20).  - 2 washes with 2X PBS

scan_protocol: After hybridization and washing, the microarray was dipped in imaging solution, covered with LifterSlip™, and then scanned using a Perkin Elmer ScanArray 4000XL and the accompanying acquisition software (ScanArray Express Microarray Analysis System v4.0). Multiple scanning at different PMT was provided for each hybridization.

data_processing:
Data extraction was carried out using CombiMatrix Microarray Imager software and a median normalization of raw medians and log2 transformation were performed using SPSS v.15.0 software. Further statistical processing was performed using the two-factor ANOVA module in the TIGR Multiple Experiment Viewer Software v4.0  (http://www.tigr.org/software/tm4/).

Hybridization signals with a variability coefficient higher than 0.5 were filtered out. A 10% cut off was applied to remove the lower tail from the low PMT distribution. Also, a 5% cut off on both tails was applied to the high PMT distribution.

label: Alexa Fluor 647

organism: Solanum lycopersicum

source_name: Red ripe fruit from tomato IL10-1 variety, biological replica 6, trial 2008

label_protocol: Total RNA (1μg) was used as a template to synthesize antisense RNA (aRNA) with the SuperScript™ Indirect RNA Amplification System Kit (Invitrogen) incorporating  Alexa Fluor 647 Reactive Dye according to manifacturer instructions.

growth_protocol: The introgression line 10-1 (IL10-1) and its parental genotypes (cv. M82) were cultivated over consecutive years in a greenhouse at the Department of Soil, Plant, Environmental and Animal Production Sciences at the University of Naples (Portici, Italy). Six plants from IL 10-1 and the parental cv. M82 were transferred into 20-cm pots containing a 1:1 mixture of medium sandy soil and compost at the beginning of March. Pots were distributed randomly 15 cm apart in rows 1 separated by a 50-cm 2 channel, and were supplemented with Nitrophoska Blu Spezial 12-12-17 (+2+20) (Compu) slow release fertilizer (5 g). Plants were watered twice daily using an automated irrigation device with 4 individual drip lines. Prior to flowering, the plants were supplied every two weeks with 30-10-10 liquid fertilizer (Grow More, USA). Fruits were collected at red-ripe stage.

extract_protocol: Total RNA was extracted from frozen, homogenized and powdered tomato fruit tissue using the CTAB (hexadecyltrimethylammonium bromide) method (Griffiths et al. J Exp Bot 50: 793–798 1999). Samples were taken from IL10-1 and M82 using three plants per genotype in the 2007 and 2008 growing trials.

treatment_protocol: Fruits were collected from IL 10-1 and its cultivated parent when 75% were full sized and red-ripe, softening had increased and the inside of the columella was completely red. Samples were generated by pooling ripe fruit from the same plant and discarding the seeds, jelly parenchyma, columella and placenta tissues. Samples were frozen under liquid nitrogen and stored at –80°C prior to homogenization in a Waring blender and processing for the extraction of ascorbic acid and total RNA.

tag: genotype

value: Introgression Line 10-1

value: epicarp and mesocarp

tag: trial

tag: plant replica


title: C2C12, dl312 infected, 24h, biological replicate 1, technical replicate A

value: myotubes

tag: time


title: IL10-1 6 2008 low pmt

description: IL10-1_6 low


title: TbPF_HCl_48h

description: Treatment with 0.31% (v/v) HCl (EC50), harvested after 48h

source_name: Procyclic Form, HCl-treated, 48h

treatment_protocol: The cells were treated with 0.31% (v/v) HCl (EC50), for a duration of 48h.


title: TbPF_DMSO_48h

description: Treatment with 3.1% (v/v) DMSO (EC50), harvested after 48h

source_name: Procyclic Form, DMSO-treated, 48h

treatment_protocol: The cells were treated with 3.1% (v/v) DMSO (EC50), for a duration of 48h.


title: IL10-1 5 2008 low pmt

description: IL10-1_5 low

source_name: Red ripe fruit from tomato IL10-1 variety, biological replica 5, trial 5008


title: IL10-1 1 2007 low pmt

description: IL10-1_1 low

source_name: Red ripe fruit from tomato IL10-1 variety, biological replica 1, trial 2007


title: IL10-1 3 2007 low pmt

description: IL10-1_3 low

source_name: Red ripe fruit from tomato IL10-1 variety, biological replica 3, trial 2007


title: IL10-1 4 2008 low pmt

description: IL10-1_4 low

source_name: Red ripe fruit from tomato IL10-1 variety, biological replica 4, trial 2008


title: IL10-1 5 2008 high pmt

description: IL10-1_5 high


title: IL10-1 1 2007 high pmt

description: IL10-1_1 high


title: IL10-1 2 2007 high pmt

description: IL10-1_2 high

source_name: Red ripe fruit from tomato IL10-1 variety, biological replica 2, trial 2007


title: IL10-1 2 2007 low pmt

description: IL10-1_2 low


title: IL10-1 3 2007 high pmt

description: IL10-1_3 high


title: IL10-1 4 2008 high pmt

description: IL10-1_4 high


title: dChip Control_13

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

description: Gene expression data from control subjects

hyb_protocol: Fragmented aRNA was hybridized to Affymetrix HG-U133 Plus 2.0 chips

scan_protocol: Standard Affymetrix protocol

data_processing: dChip

source_name: Control

label_protocol: total RNA was converted to amplified RNA (aRNA) and fragmented using the MessageAmpTM III RNA amplification kit

extract_protocol: Total RNA was extracted from whole-blood using the Paxgene Blood RNA Kit

tag: disease

value: Control subject

value: Whole blood


title: dChip Control_19

tag: tissue


title: dChip Control_14


title: dChip Control_21


title: dChip Control_16


title: dChip Control_15


title: dChip Control_12


title: dChip Control_20


title: dChip Control_3


title: dChip Control_5


title: dChip Control_17


title: dChip Control_11


title: dChip Control_9


title: dChip Control_18


title: dChip Control_4


title: dChip PMF_9

description: Gene expression data from patients with Primary Myelofibrosis (PMF)

source_name: Primary Myelofibrosis (PMF)

value: Myeloproliferative Disorder (MPD)


title: dChip PMF_7


title: dChip Control_1


title: dChip Control_10


title: dChip Control_7


title: dChip Control_2


title: dChip PMF_8


title: dChip Control_6


title: dChip Control_8


title: dChip PMF_6


title: dChip PMF_4


title: Mouse number 1982

city: Toronto

first: Sean

middle: Eoin

last: Egan

state: Ontario

address: 101 College Street, rm 14-309

department: Program in Developmental and Stem Cell Biology

institute: The Hospital for Sick Children

description:
Tumor DNA is being compared to control DNA from the same animal
M1M_081010R_SE3_1982_252741410151_S01_CGH_105_Jan09.txt

hyb_protocol: 2 ug of each DNA sample was hybridized according to the 40-hour manual protocol described by the manufacturer

scan_protocol: The arrays were scanned at 5 micron resolution in an Agilent scanner

data_processing: The images were processed with Agilent feature extraction version 9.5.1.1

source_name: Lfng conditional mutant non-tumor gDNA

label_protocol: The Invitrogen BioPrime CGH labeling kit was used (Cat#18094011) according to manufacturer's protocol

extract_protocol: Genomic DNAs were purified using DNAeasy kits (Qiagen) combined with phenol-chloroform extraction.

value: FVB

tag: identifier

value: Mouse number 1982

tag: reference type

value: non-tumor, control DNA

source_name: Lfng conditional mutant mouse mammary tumor

tag: mammary tumor type

value: Glandular Basal-like tumor (Type I)


title: N2A Pbcas4 shRNA rep3

source_name: N2A transfect with mouse Pbcas4 specific shRNA


title: dChip PMF_3


title: dChip PMF_2


title: dChip PMF_1


title: Mouse number 8802

description:
Tumor DNA is being compared to control DNA from the same animal
M1M_081010R_SE5_8802_252741410153_S01_CGH_105_Jan09.txt

value: Mouse number 8802


title: dChip PV_39

description: Gene expression data from patients with Polycythemia Vera (PV)

source_name: Polycythemia Vera (PV)


title: dChip PMF_5


title: dChip PV_41


title: Mouse number 8733

description:
Tumor DNA is being compared to control DNA from the same animal
M1M_081010R_SE4_8733_252741410152_S01_CGH_105_Jan09.txt

value: Mouse number 8733


title: Mouse number 1981

description:
Tumor DNA is being compared to control DNA from the same animal
M1M_081010R_SE2_1981_252741410150_S01_CGH_105_Jan09.txt

value: Mouse number 1981

value: EMT/Spindle type tumor


title: dChip PV_37


title: dChip PV_33


title: dChip PV_40


title: dChip PV_34


title: dChip PV_38


title: dChip PV_30


title: dChip PV_31


title: dChip PV_25


title: dChip PV_23


title: dChip PV_29


title: dChip PV_27


title: dChip PV_22


title: dChip PV_24


title: dChip PV_28


title: dChip PV_35


title: dChip PV_36


title: Mouse number 1330

description:
Tumor DNA is being compared to control DNA from the same animal
M1M_081010R_SE1_1330_252741410149_S01_CGH_105_Jan09.txt

value: Mouse number 1330

source_name: Lfngflox/+; MMTV-Cret mouse mammary tumor

value: Mixed tumor histology


title: dChip PV_26


title: dChip PV_32


title: dChip PV_19


title: dChip PV_18


title: dChip PV_15


title: dChip PV_20


title: dChip PV_16


title: dChip PV_12


title: dChip PV_13


title: dChip PV_9


title: dChip PV_14


title: dChip PV_17


title: dChip ET_18

description: Gene expression data from patients with Essentiel Thrombocythemia (ET)

source_name: Essentiel Thrombocythemia (ET)


title: dChip PV_10


title: dChip PV_2


title: dChip PV_1


title: dChip PV_3


title: dChip PV_11


title: dChip ET_19


title: dChip ET_14


title: dChip PV_8


title: dChip PV_7


title: dChip PV_5


title: dChip PV_4


title: dChip ET_13


title: dChip ET_17


title: dChip ET_15


title: dChip ET_11


title: dChip ET_16


title: dChip ET_12


title: dChip PV_6


title: dChip ET_9


title: dChip ET_10


title: dChip ET_4


title: dChip ET_7


title: dChip ET_5


title: dChip ET_6


title: dChip PV_21


title: dChip ET_8


title: dChip ET_3


title: dChip ET_1


title: dChip ET_2


title: liver STZ 0.5% phloridzin diet rep4

city: Tsukuba

first: Masuko

last: Kobori

state: Ibaraki

address: 2-1-13 Kannondai

institute: Food Research Institute, National Agriculture and Food Research Organization

description: Gene expression data from STZ-treated mouse liver after 14 day feeding of 0.5% phloridzin diet

hyb_protocol: Fifteen microgram aliquots of fragmented cRNA were hybridized to an array (Mouse Genome 430 2.0 array, Affymetrix) at 45°C for 16 h.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.3 (Affymetrix).

data_processing: Data analysis was performed with a GeneChip Operating Software (Ver. 1.3) using Affymetrix default analysis settings and global scaling as normalization method..

source_name: liver, STZ-treated fed 0.5% phloridzin diet for 14 days

label_protocol: Double-stranded cDNA was synthesized from the total RNA of each mouse using the One-Cycle cDNA Synthesis Kit (Affymetrix Japan KK, Tokyo, Japan) with a T7-(dT)24 primer. Biotin-labeled cRNA was then synthesized using an IVT Labeling Kit (Affymetrix). The biotin-labeled cRNA was further purified and fragmented using the Sample Cleanup Module (Affymetrix).

growth_protocol: Six-week-old male BALB/c mice were obtained from the Institute for Animal Reproduction, Charles River Japan Inc. (Ibaraki, Japan). The mice were housed under conditions of 24± 1°C, 55 ± 5% humidity, and 12 hour light/dark photocycles (dark period from 0800 to 2000) with free access to water and a standard nonpurified diet (NMF, Oriental Yeast Co., Tokyo, Japan) for a week prior to the experiment.

extract_protocol: The mice were killed under anesthesia with pentobarbital, and blood and liver tissue were immediately collected. Total RNA was extracted from liver tissues using an RNeasy Midi Kit (Qiagen KK, Tokyo, Japan) according to the manufacturer’s instructions.

treatment_protocol: The mice were then intraperitoneally injected with STZ (Wako Pure Chemical Industries, Osaka, Japan, 185 mg/kg in 0.05M citrate buffer, pH 4.5).  Mice (n=6) in the untreated control group did not receive any treatment.  Tail vein blood was sampled weekly and the blood glucose levels of the samples were immediately measured using a blood glucose test meter (Glucocard, Arkray, Kyoto, Japan).  After 1 week, 18 mice showing non-fasting blood glucose levels of 330-590 mg/dL were divided into 3 groups: one group was fed with AIN93G only (control group), the others with an AIN93G diet containing 0.1% or 0.5% phloridzin (Funakoshi, Tokyo, Japan) for 2 weeks. All mice had access to food and water ad libitum during the experimental period.

tag: gender

value: male

value: BALB/c

value: liver

tag: diet

value: STZ-treated and AIN93G diet with 0.5% phloridzin for 14 days


title: liver STZ 0.5% phloridzin diet rep3


title: liver STZ 0.5% phloridzin diet rep5


title: liver STZ 0.1% phloridzin diet rep5

description: Gene expression data from STZ-treated mouse liver after 14 day feeding of 0.1% phloridzin diet

source_name: liver, STZ-treated fed 0.1% phloridzin diet for 14 days

value: STZ-treated and AIN93G diet with 0.1% phloridzin for 14 days


title: JAZ8deltaC mock rep2

city: miki

first: kenji

last: gomi

state: kagawa

institute: Kagawa University

description: gene expression after 24 hr in mock-treated transgenic rice leaf blades

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rice Oligo Microarrays for 17 hours at 65 ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides.

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

organism: Oryza sativa

source_name: Transgenic Rice leaf blades without treatment, replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using an Agilent Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Rice plants were grown from seed in growthchamber [25 ºC, 60 - 80% relative humidity (RH)].

extract_protocol: Total RNA from rice was extracted from leaf blades after each treatment using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Four -leaf-stage rice plants were treated with 100μM jasmonate for 1 day at 25 ºC.

value: JAZ8deltaC transgenic

tag: cultivar

value: Nipponbare

tag: developmental stage

value: four-leaf-stage

value: fourth-leaf blade

value: mock


title: JAZ8deltaC mock rep3

source_name: Transgenic Rice leaf blades without treatment, replicate3


title: JAZ8deltaC JA rep2

description: gene expression after 24 hr in jasmonate-treated transgenic rice leaf blades

source_name: Transgenic Rice leaf blades treated with 100 μM jasmonate, replicate2

value: jasmonate


title: JAZ8deltaC JA rep1

source_name: Transgenic Rice leaf blades treated with 100 μM jasmonate, replicate1


title: JAZ8deltaC JA rep4

source_name: Transgenic Rice leaf blades treated with 100 μM jasmonate, replicate4


title: JAZ8deltaC mock rep4

source_name: Transgenic Rice leaf blades without treatment, replicate4


title: liver STZ 0.5% phloridzin diet rep1

tag: strain


title: liver STZ 0.5% phloridzin diet rep2


title: JAZ8deltaC JA rep3

source_name: Transgenic Rice leaf blades treated with 100 μM jasmonate, replicate3


title: WT JA rep4

description: gene expression after 24 hr in jasmonate-treated rice leaf blades

source_name: Rice leaf blades treated with 100 μM jasmonate, replicate4

value: WT


title: liver STZ 0.1% phloridzin diet rep4


title: JAZ8deltaC mock rep1

source_name: Transgenic Rice leaf blades without treatment, replicate1


title: WT JA rep3

source_name: Rice leaf blades treated with 100 μM jasmonate, replicate3


title: WT JA rep2

source_name: Rice leaf blades treated with 100 μM jasmonate, replicate2


title: WT JA rep1

source_name: Rice leaf blades treated with 100 μM jasmonate, replicate1


title: WT mock rep3

description: gene expression after 24 hr in mock-treated rice leaf blades

source_name: Rice leaf blades without treatment, replicate3


title: WT mock rep1

source_name: Rice leaf blades without treatment, replicate1


title: V19-OSKM MEF Utx KO no DOX

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: Gene expression data of the indicated cell line

hyb_protocol: Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.

data_processing: The data were analyzed with Affy Expression Console software, using RMA method. Probes were further filtered to include only probes that have at least one call > 6 (in log2-scale)

source_name: V19-OSKM MEF Utx -/Y (no DOX)

label_protocol: 250 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: N2B27 2i/LIF mouse ESC media

extract_protocol: mRNA was extracted byTRIZOL reagent (invitogene) according to manufacturer's instructions

treatment_protocol: Cells were washed with PBS and then harvested by trypsinization for RNA extraction

tag: cell type

value: Mouse Embryonic Fibroblast Cells (MEFs)

tag: genotype/variation

value: UTX-/Y (KO)

tag: dox induction

value: no


title: liver STZ 0.1% phloridzin diet rep1


title: liver STZ 0.1% phloridzin diet rep3


title: WT mock rep2

source_name: Rice leaf blades without treatment, replicate2

tag: genotype

tag: treatment


title: liver STZ 0.1% phloridzin diet rep2

source_name: liver, STZ-treated fed 0.1% phloridzin diet for 14 days


title: OSKM_MEF_Nanog_KO

value: Mouse Embryonic Fibroblast Cells (MEF) generated from Nanog-/- ESCs (Mitsui et al. Cell 2003)

value: transduced with OSKM lentivirus for 8 days


title: WT mock rep4

source_name: Rice leaf blades without treatment, replicate4


title: V19-OSKM MEF Utx WT no DOX

source_name: V19-OSKM MEF Utx +/Y (no DOX)

value: UTX+/Y (WT)


title: V19-OSKM MEF Utx KO + DOX

source_name: V19-OSKM MEF Utx -/Y (++ DOX)

value: yes


title: mes-2; mes-4 v wt 4

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

description: Biological replicate 4 of 4.  Mutant and wild type dissected germ lines grown at 20 deg.

hyb_protocol: Hybridization buffer (Genisphere 2X fromamide hyb buffer) and KREAblock were added, and samples were applied to microarrays enclosed in Die-Tech hyb chambers. After hybridization, slides were washed sequential with 2X SSC/0.2% SDS, 2X SSC and 0.2X SSC.

scan_protocol: Scanned on an GenePix 4000B scanner.

data_processing: Signal from each channel was background subtracted and log2 of test (mt) sample signal over reference (wt) sample signal was obtained. log 2 ratios were print-tip LOWESS normalized, then global scale normalized using median absolut deviation. Bioconductor package marray was used for all processing.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: mes-2; mes-4 mutant dissected germ lines

label_protocol: aRNA was labeled using Kreatech ULS-Cy 3/5 aRNA Labeling Kit (Open Biosystems) and then fragmented using  Ambion Fragmentation Reagents

growth_protocol: Worms were grown to the adult stage. For wild type, mes-2, and mes-4, germ lines were dissected from adults containing no more than a few fertilized embryos. For mes-2; mes-4, well proliferated germ lines with oocytes were collected.

extract_protocol: Total RNA was extracted using Trizol reagent, then amplified poly-A RNA was made using the MessageAmp II aRNA Amplification Kit (Ambion)

tag: Stage

value: adult germ lines

tag: temperature

value: 20 degrees

source_name: wild type dissected germ lines


title: liver STZ treated diabetic rep3

description: Gene expression data from STZ-treated mouse liver after 14 day feeding of control AIN93G diet

source_name: liver, STZ-treated fed AIN93G diet for 14 days

value: male

value: BALB/c

value: liver

value: STZ-treated fed AIN93G diet for 14 days


title: liver STZ treated diabetic rep4


title: mes-2; mes-4 v wt 3

description: Biological replicate 3 of 4.  Mutant and wild type dissected germ lines grown at 20 deg.


title: liver STZ treated diabetic rep5


title: mes-4 v wt 4

source_name: mes-4 mutant dissected germ lines


title: mes-2; mes-4 v wt 2

description: Biological replicate 2 of 4.  Mutant and wild type dissected germ lines grown at 20 deg.


title: mes-4 v wt 3


title: liver STZ treated diabetic rep2


title: mes-2; mes-4 v wt 1

description: Biological replicate 1 of 4.  Mutant and wild type dissected germ lines grown at 20 deg.


title: mes-4 v wt 2


title: mes-4 v wt 1


title: non STZ liver control diet rep3

description: Gene expression data from liver after 14 day feeding of control AIN93G diet

source_name: liver, fed control AIN93G diet for 14 days

value: AIN93G diet for 14 days


title: non STZ liver control diet rep4


title: mes-2 v wt 3

source_name: mes-2 mutant dissected germ lines


title: non STZ liver control diet rep2


title: mes-2 v wt 2


title: mes-2 v wt 4


title: non STZ liver control diet rep1


title: liver 1.0% quercetin diet rep2

description: Gene expression data from liver after 14 day feeding of 1.0% quercetin diet

source_name: liver, fed 1% quercetin diet for 14 days

treatment_protocol: The mice were then fed for 2 weeks with AIN93G (control group) or AIN93G containing 0.1%, 0.5% or 1% quercetin.

value: AIN93G with 1.0% quercetin diet for 14 days


title: liver 1.0% quercetin diet rep5