title: Series 1 Day 4 Dusk

description:
Paired dye-flipped arrays.
252985410006_201108021030_S01_GE2_107_Sep09_1_1.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410009_201108021057_S01_GE2_107_Sep09_1_3.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells Day 4 Dusk


title: Series 1 Day 2 Dawn

status: Public on Apr 18 2013

type: RNA

city: Seattle

first: Justin

last: Ashworth

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

description:
Paired dye-flipped arrays.
252985410005_201108021044_S01_GE2_107_Sep09_1_2.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410008_201108021111_S01_GE2_107_Sep09_1_4.txt: Cy5-labeled sample and Cy3-labeled reference.

hyb_protocol: Array slides were hybridized with equal amounts of oppositely labeled sample and internal reference RNA according to standard Agilent array hybridization protocols.

scan_protocol: Arrays slides were scanned using an Agilent two-color microarray slide scanner.

data_processing:
Two-color expression data were processed using the limma package in R for Agilent two-color microarray data. This included background correction (normexp method), within-array normalization (loess method), and between-array normalization (Aquantile method). Expression ratios were calculated relative to the mean within-experiment expression level for each probe in order to remove batch effects between experiments.
Two sets of value columns are included in the value Matrix (see supplemental 'value_Matrix' file). The first set of values (also used in the VALUE column of below sample tables) contain the normalized log2 ratios for each gene within each growth series (labels: X400/800.Day#.Dk/Lt). The second set of values are log2 ratios for merged, paired samples from each growth series, as derived from the first of values (labels: Day#.Lt/Dk). The first set of values was used for statistical analysis. The second set of (derived) values is provided for the purposes of simplicity, illustration and reference. Separating these two sets of expression values are boolean (TRUE/FALSE) columns indicating the significance of association for each gene with four experimental conditions (as indicated by characteristics in the metadata) by two-factor ANOVA with a permuted p-value cutoff of 0.01.

molecule: total RNA

organism: Thalassiosira pseudonana CCMP1335

source_name: Filtered cells Day 2 Dawn

label_protocol: Transcribed mRNA was amplified and labeled using the Agilent Quick-Amp Labeling Kit (two-color).

growth_protocol: Axenic cultures of Thalassiosira pseudonana CCMP1335 (Provasoli-Guillard National Center for Culture of Marine Phytoplankton) were grown in ESAW medium modified with lower levels of nitrate (80 µM), silicic acid (110 µM) and phosphate (20 µM) and grown in bioreactors. Prior to the experiment, the diatoms were acclimated to constant 20°C temperature and ambient CO2 under a 12hr:12hr dark:light diurnal cycle at 125 µmol photons m-2 s-1 of photosynthetically active radiation (PAR) provided by fluorescent lamps. Cultures were considered acclimated when the growth rates of three consecutive growth curves were significantly equal to each other. Chemicals were purchased from Sigma–Aldrich (St. Louis, MO). During the experiments the bioreactors were equilibrated at ambient (400 ppm) or elevated (800 ppm) CO2 by bubbling of mixed gasses (2L/min) and stirring (50 rpm) in a 10L glass bioreactor system (BioFlow). CO2-scrubbed ambient air and pure CO2 gas were mixed and regulated using two mass-flow controller/monitors (G265, Qubit Systems, Inc., Kingston, Canada) and solenoid controller.

extract_protocol: Total RNA was extracted using the mirVANA kit from Invitrogen (total RNA extraction protocol).

treatment_protocol: Cells (approx. 3x10^7) were harvested by filtration (30-200mL) and flash-frozen.

tag: condition

value: Dawn

tag: growth phase

value: Exponential

tag: co2 gas input

source_name: common internal reference sample

tag: reference

value: common internal reference sample


title: Pool for sample 13

type: genomic

city: Logroño

first: Ramon

last: Gonzalez

address: C. Madre de Dios, 51

department: Instituto de Ciencias de la Vid y del Vino

country: Spain

institute: Consejo Superior de Investigaciones Científicas

description:
HIP 3 t=0 F2
Control for competition 13

hyb_protocol: Reactions hybridized overnight to custom-built TAG4 microarrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450   according to [Pierce SE, Davis RW, Nislow C, Giaever G (2007) Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat Protocols 2: 2958-2974]

scan_protocol: GeneChips were scanned at an emission wavelength of 560 nm using a GeneChip scanner (Affymetrix).

data_processing: Data procesing was performed according to [Pierce SE, Davis RW, Nislow C, Giaever G (2007) Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat Protocols 2: 2958-2974]. Perl scripts were downloaded from the supplementary web [Pierce, S.E. et al. A unique and universal molecular barcode array. Nat. Methods 3, 601-603 (2006)]. Data were normalized by quantile. Extracted data are in natural scale, but Ratios used for discussion in the associated manuscript are expressed in log2.

label: biotin

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Initial pool for competition 13

label_protocol: Amplification of the barcodes (uptags and downtags), with simoultaneous labelling using biotinilated primers was performed according to [Pierce SE, Davis RW, Nislow C, Giaever G (2007) Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat Protocols 2: 2958-2974]

growth_protocol: Bioreactors containing 200 mL of the previously described synthetic must were inoculated to an initial OD600 of 0.2. Cultures were grown in batch mode during about 12 h prior to triggering the continuous cultures. According to the data obtained from batch characterization, dilution rate was set to 0.23 h-1 for competitions mimicking Phase I and to 0.04 h-1 for those mimicking Phase II. Competition experiments using the heterozygous collection were run for 20 generations (corresponding to 60 h for Phase I or 347 h for Phase II) while those performed with the homozygous collection were run for 10 generations (30 h for Phase I or 174 h for Phase II). Yeast cell samples were taken at the onset of the continuous cultures, and after the indicated numbers of generations, in order to compare pool compositions at the beginning and the end of the competition experiments. Additional triplicate competition experiments, using YPD broth (D=0.23 h-1), were performed in order to differentiate deletions unspecifically affecting yeast growth from those specific for Phase I or Phase II fermentation conditions.

extract_protocol: Genomic DNA was extracted bu using the YeaStarTM Genomic DNA Kit (Zymo Research).

tag: yeast collection

value: Whole genome heterozygous deletion collection

tag: phase or medium

value: Preculture

tag: number of generations


title: Series 1 Day 3 Dusk

description:
Paired dye-flipped arrays.
252985410006_201108021030_S01_GE2_107_Sep09_1_3.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410008_201108021111_S01_GE2_107_Sep09_1_1.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells Day 3 Dusk

value: Dusk

value: Stationary


title: Pool for sample 14

description:
HIP 4 t=0 F2
Control for competition 14

source_name: Initial pool for competition 14


title: Series 1 Day 4 Dawn

description:
Paired dye-flipped arrays.
252985410006_201108021030_S01_GE2_107_Sep09_1_2.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410009_201108021057_S01_GE2_107_Sep09_1_4.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells Day 4 Dawn


title: Series 1 Day 2 Dusk

description:
Paired dye-flipped arrays.
252985410005_201108021044_S01_GE2_107_Sep09_1_1.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410008_201108021111_S01_GE2_107_Sep09_1_3.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells Day 2 Dusk


title: Enrichment Environment-Clean Air 3-2

city: Shiga

first: Satoshi

last: Yokota

address: 1-1-1 Noji-Higashi, Kusatsu

country: Japan

institute: Ritsumeikan University

description: Gene expression in the olfactory bulb of mouse reared in enrichment environment and then housed in clean air chamber

hyb_protocol: Hybridizations were performed for 17 hrs, according to the manufacturer’s protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 micron resolution.

data_processing: Images were quantified using Agilent Feature Extraction software version 10.7.3.1

organism: Mus musculus

source_name: Reared in enrichment environment and housed in clean air

label_protocol: RNA was labeled with Cy3-CTP using the Agilent’s Low Input Quick Amp Labeling Kit following the manufacturers protocol. Labeled cRNA was assessed using the Nanodrop ND-1000 UV-VIS Spectrophotometer version 3.8.0. (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent SurePrint G3 Mouse GE 8×60K microarray.

growth_protocol: Pregnant C57BL/6J mice, weighing approximately 30 g (Figure S1A) at gestational day 14, were purchased from CLEA Japan, Inc. (Tokyo, Japan) and used for experiments. All animals were acclimated to our animal room (The Center for Environmental Health Science for the Next Generation, Research Institute for Science and Technology, Tokyo University of Science). They had free access to water and standard animal food and were exposed to a 12-hour light/dark cycle (lights on between 8:00 and 20:00), a temperature of 22±1 °C, and a humidity-controlled environment (50±5%).

extract_protocol: Total RNA was isolated using Isogen (Nippon Gene Co., Ltd., Tokyo, Japan) according to the manufacturer's protocol and suspended in pure water. The RNA quantity was determined by spectrophotometry measurement of OD260/280 (ratio > 1.8) in a BioPhotometer plus (Eppendorf, Hamburg, Germany). After purification of RNA by ethanol precipitation and an RNeasy Micro Kit (Qiagen, Hilden, Germany), the RNA integrity was evaluated by capillary electrophoresis using a Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA).

treatment_protocol: Upon arrival to the colony, half of the pregnant dams were assigned to the standard cage environment (C) and the other half to environmental enrichment (EE). Standard laboratory cage consisted of a common housing cage for mice (30 × 20 × 12.5 cm: 7500 cm3). Environmental enrichment consisted of a larger (40 × 25 × 19 cm: 19,000 cm3) cage containing a running wheel, small house, wood blocks, and plastic tubing that were moved to different locations within each cage every 2–3 days and were exchanged with new toys. One dam and her pups (n=8) were housed in either the standard laboratory cage or environmental enrichment throughout the perinatal period and until weaning. After weaning at postnatal day 27, the offspring mice were placed in a control chamber or DE inhalation chamber and were housed under the same conditions as during the perinatal period. The mice were exposed to DE for 8 hours/day (10:00–18:00) for 28 days (postnatal days 28−55) in the control or DE inhalation chamber at the Center for Environmental Health Science for the Next Generation (Research Institute for Science and Technology, Tokyo University of Science). Housing environment (standard cage environment [C] or environmental enrichment [EE]) during the perinatal period (gestational day 14–postnatal day 28) and chamber (control [C] and [DE]) established four experimental groups: C-C, C-DE, EE-C, and EE-DE (Figure 1). Necropsies were performed 1 day after the final exposure. The olfactory bulb was collected from each male mouse, frozen quickly in liquid nitrogen, and then stored at −80 °C until total RNA extraction. Lung tissues were also collected and immersed in 10% phosphate buffered formalin until use.

tag: tissue

value: olfactory bulb

tag: strain

tag: housing environment

value: enrichment environment

tag: chamber treatment

value: clean air


title: HIP YPD rep2

description:
HIP 4 YPD 20
Competition for 20 generations of the whole genome heterozygous yeast deletion collection in YPD

source_name: Heterozygous collection competition in YPD for 20 generations

value: YPD


title: Series 1 Day 1 Dawn

description:
Paired dye-flipped arrays.
252985410005_201108021044_S01_GE2_107_Sep09_1_4.txt: Cy3-labeled sample and Cy5-labeled common reference.
252985410007_201108021125_S01_GE2_107_Sep09_1_2.txt: Cy5-labeled sample and Cy3-labeled reference.

source_name: Filtered cells Day 1 Dawn


title: Standard Cage-Diesel Exhaust 2-2

description: Gene expression in the olfactory bulb of mouse reared in standard cage and then exposed to diesel exhaust

source_name: Reared in standard cage and then reveived diesel exhaust inhalation

value: standard cage

value: diesel exhaust inhalation


title: Enrichment Environment-Diesel Exhaust 4-2

description: Gene expression in the olfactory bulb of mouse reared in enrichment environment and then exposed to diesel exhaust

source_name: Reared in enrichment environment and then reveived diesel exhaust inhalation


title: HIP YPD rep3

description:
HIP YPD 20
Competition for 20 generations of the whole genome heterozygous yeast deletion collection in YPD


title: Pool for samples 8 and 11

description:
HIP t=0
Control for competitions 8 and 11

source_name: Initial pool for competitions 8 and 11


title: Enrichment Environment-Diesel Exhaust 4-1


title: Pool for sample 12

description:
HIP 2 t=0 F2
Control for competition 12

source_name: Initial pool for competition 12


title: Standard Cage-Clean Air 1-2

description: Gene expression in the olfactory bulb of mouse reared in standard cage and then housed in clean air chamber

source_name: Reared in standard cage and housed in clean air


title: HIP YPD rep1

description:
HIP 3 YPD 20
Competition for 20 generations of the whole genome heterozygous yeast deletion collection in YPD


title: Enrichment Environment-Clean Air 3-1


title: Standard Cage-Diesel Exhaust 2-1


title: Pool for samples 6,7, 9 and 10

description:
HIP 3-4 Precultivo.t=0
Control for competitions 6,7, 9 and 10

source_name: Initial pool for competitions 6,7, 9 and 10


title: timepoint 2 hrs; pig 3 Salmonella Cy3 vs pig 2 Salmonella Cy5

status: Public on Apr 17 2013

city: Lelystad

first: Marcel

last: Hulst

state: Flevoland

address: Edelhertweg 15

department: Livestock research

country: Netherlands

institute: Animal Sciences Group

description: slide 433: 2 hours; pig 3 Salmonella-fluorescein/Cy3 vs pig 2 Salmonella-biotin/Cy5; dye-swap: slide 432

hyb_protocol: according to manufacturer's recommendations: RNA MICROMAX TSA labeling and detection kit (Perkin-Elmer, Zoetermeer, The Netherlands)

scan_protocol: scanned on GenePix 4200A 01 Autoloader [116826] (Molecular Devices, Apeldoorn, The Netherlands) image processed with GenePix 4200A 01 Autoloader [116826] (Molecular Devices, Apeldoorn, The Netherlands)

data_processing: data processing in GenePix Pro 6.1.0.4 or  6.0.1.25 (Molecular Devices, Apeldoorn, The Netherlands), data normalization (blank-specific background correction, LOWESS fit function with a fraction of 0.2) using a customized version of the statistical software package R, simultaneous data analysis of dye-swaps.

organism: Sus scrofa

source_name: Total RNA of scraping from Salmonella infected jejunal segment of pig 3 perfused for 2 hours

label_protocol: 4 µg of RNA template was labeled with fluorescein or biotin, RNA MICROMAX TSA labeling and detection kit (Perkin-Elmer, Zoetermeer, The Netherlands)

extract_protocol: Trizol extraction + additional steps to remove proteoglycan and polysaccharide contaminations + DNAse treatment

treatment_protocol: pig jejunal segment perfused with bacterial suspension of Salmonella, sampling of scrapings after 2 hours additional perfusion

tag: subject

value: pig 3

value: jejunum

tag: time

value: 2 hours perfusion

tag: infection

value: Salmonella enterica serovar typhimurium DT104

source_name: Total RNA of scraping from Salmonella infected jejunal segment of pig 2 perfused for 2 hours

value: pig 2


title: timepoint 4 hrs; pig 2 Salmonella Cy3 vs pig 4 Salmonella Cy5

description: slide 440: 4 hours; pig 2 Salmonella-fluorescein/Cy3 vs pig 4 Salmonella-biotin/Cy5; dye-swap: slide 827

source_name: Total RNA of scraping from Salmonella infected jejunal segment of pig 2 perfused for 4 hours

treatment_protocol: pig jejunal segment perfused with bacterial suspension of Salmonella, sampling of scrapings after 4 hours additional perfusion

value: 4 hours perfusion

source_name: Total RNA of scraping from Salmonella infected jejunal segment of pig 4 perfused for 4 hours

value: pig 4


title: timepoint 4 hrs; pig 3 Salmonella Cy3 vs pig 2 Salmonella Cy5

description: slide 828: 4 hours; pig 3 Salmonella-fluorescein/Cy3 vs pig 2 Salmonella-biotin/Cy5; dye-swap: slide 115

source_name: Total RNA of scraping from Salmonella infected jejunal segment of pig 3 perfused for 4 hours


title: timepoint 4 hrs; pig 2 Salmonella Cy3 vs pig 3 Salmonella Cy5

description: slide 115: 4 hours; pig 2 Salmonella-fluorescein/Cy3 vs pig 3 Salmonella-biotin/Cy5; dye-swap: slide 828


title: timepoint 4 hrs; pig 4 Salmonella Cy3 vs pig 2 Salmonella Cy5

description: slide 827: 4 hours; pig 4 Salmonella-fluorescein/Cy3 vs pig 2 Salmonella-biotin/Cy5; dye-swap: slide 440


title: timepoint 2 hrs; pig 4 Salmonella Cy3 vs pig 3 Salmonella Cy5

description: slide 437: 2 hours; pig 4 Salmonella-fluorescein/Cy3 vs pig 3 Salmonella-biotin/Cy5; dye-swap: slide 436

source_name: Total RNA of scraping from Salmonella infected jejunal segment of pig 4 perfused for 2 hours


title: timepoint 2 hrs; pig 2 Salmonella Cy3 vs pig 4 Salmonella Cy5

description: slide 438: 2 hours; pig 2 Salmonella-fluorescein/Cy3 vs pig 4 Salmonella-biotin/Cy5; dye-swap: slide 439


title: timepoint 2 hrs; pig 2 Salmonella Cy3 vs pig 3 Salmonella Cy5

description: slide 432: 2 hours; pig 2 Salmonella-fluorescein/Cy3 vs pig 3 Salmonella-biotin/Cy5; dye-swap: slide 433


title: timepoint 2 hrs; pig 3 Salmonella Cy3 vs pig 4 Salmonella Cy5

description: slide 436: 2 hours; pig 3 Salmonella-fluorescein/Cy3 vs pig 4 Salmonella-biotin/Cy5; dye-swap: slide 437


title: timepoint 4 hrs; pig 3 Salmonella Cy3 vs pig 4 Salmonella Cy5

description: slide 442: 4 hours; pig 3 Salmonella-fluorescein/Cy3 vs pig 4 Salmonella-biotin/Cy5; dye-swap: slide 443


title: timepoint 2 hrs; pig 4 Salmonella Cy3 vs pig 2 Salmonella Cy5

description: slide 439: 2 hours; pig 4 Salmonella-fluorescein/Cy3 vs pig 2 Salmonella-biotin/Cy5; dye-swap: slide 438


title: timepoint 4 hrs; pig 4 Salmonella Cy3 vs pig 3 Salmonella Cy5

description: slide 443: 4 hours; pig 4 Salmonella-fluorescein/Cy3 vs pig 3 Salmonella-biotin/Cy5; dye-swap: slide 442


title: timepoint 8 hrs; pig 4 Mock Cy3 vs pig 4 Salmonella Cy5

description: slide 008: 8 hours pig 4; Mock-fluorescein/Cy3 vs Salmonella-biotin/Cy5; dye-swap: slide 009

source_name: Total RNA of scraping from mock infected jejunal segment of pig 4 perfused for 8 hours

treatment_protocol: pig jejunal segment perfused without bacterial suspension, sampling of scrapings after 8 hours additional perfusion

value: 8 hours perfusion

value: mock infected

source_name: Total RNA of scraping from Salmonella infected jejunal segment of pig 4 perfused for 8 hours

treatment_protocol: pig jejunal segment perfused with bacterial suspension of Salmonella, sampling of scrapings after 8 hours additional perfusion


title: timepoint 8 hrs; pig 3 Mock Cy3 vs pig 3 Salmonella Cy5

description: slide 028: 8 hours pig 3; Mock-fluorescein/Cy3 vs Salmonella-biotin/Cy5; dye-swap: slide 033

source_name: Total RNA of scraping from mock infected jejunal segment of pig 3 perfused for 8 hours

source_name: Total RNA of scraping from Salmonella infected jejunal segment of pig 3 perfused for 8 hours


title: timepoint 8 hrs; pig 4 Salmonella Cy3 vs pig 4 Mock Cy5

description: slide 009: 8 hours pig 4; Salmonella-fluorescein/Cy3 vs Mock-biotin/Cy5; dye-swap: slide 008


title: Pooled ON

city: Iowa City

first: Alex

middle: Handler

last: Wagner

state: Iowa

address: 5315 Seamans Center

department: Biomedical Engineering

institute: University of Iowa

description: Pooled from six donors

hyb_protocol: The resulting biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Human Exon 1.0 ST Arrays, and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data collected using the GeneChip operating software (GCOS) v1.4.

data_processing:
Ten Affymetrix GeneChip Human Exon 1.0 ST (HuEx 1.0) microarrays were simultaneously normalized using the Affymetrix Power Tools (APT) probeset summarization tool.  Normalization was done at both the probeset and metaprobeset level using the PLIER-sketch method with GC-background correction.
HuEx-1_0-st-v2.r2.dt1.hg18.core.ps
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

organism: Homo sapiens

source_name: optic nerve ON

label_protocol: Four ug of SPIA amplified DNA was then used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.  Five micrograms of this product was fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

extract_protocol: Total RNA was extracted using Trizol Plus RNA Purification kits (Invitrogen) as previously described by Wang W-H, et al.

treatment_protocol: Human donor eyes (20 normal donors) were obtained from the Lions Eye Institute for Transplant and Research (Tampa, FL) and stored in RNALater (Invitrogen) at 4 °C for up to 30 d. Tissue was dissected under a microscope into cornea, iris, ciliary body, trabecular meshwork, lens, retina, choroid/RPE, sclera, optic nerve, and optic nerve head, and stored at -80 °C.

value: optic nerve ON


title: timepoint 8 hrs; pig 2 Salmonella Cy3 vs pig 2 Mock Cy5

description: slide 118: 8 hours pig 2; Salmonella-fluorescein/Cy3 vs Mock-biotin/Cy5; dye-swap: slide 117

source_name: Total RNA of scraping from Salmonella infected jejunal segment of pig 2 perfused for 8 hours

source_name: Total RNA of scraping from mock infected jejunal segment of pig 2 perfused for 8 hours


title: HCT116 Top1 siRNA - experiment 2

city: Fairfax

first: Michael

last: Ryan

state: VA

address: 11781 Lee Jackson Hwy, Ste 320

institute: In Silico Solutions

description: HCT116 cells transfected with a Top1 siRNA

hyb_protocol: The array work was done by a core facility according to the Affymetrix standard protocol for exon arrays.

data_processing: The processed data files contain comma separated probe values normalized by RMA and quantile normalization.  R, Bioconductor, and the exon.pmcdf package were used for normalization.  We work in this study with probe-level values so probeset aggregations are not provided.

source_name: cell line - HCT116

growth_protocol: Human HCT116 and MCF7 cell lines were obtained from ATCC (Rockville, MD) and grown in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Gemini Bio-products, West Sacramento, CA) at 37 degrees Celsius in 95% air and 5% CO2.

extract_protocol: RNA extraction was performed with the “Nucleospin RNA II” kit (Macherey-Nagel, Bethlehem, PA).

treatment_protocol: HCT116 cells were treated with CPT (10 uM) for 1, 2, 4, 15 and 20 hours. Controls samples were analyzed at 4 and 20 h following DMSO treatment (0.1%; the solvent used to dissolve CPT). MCF7 cells were treated with CPT (10 uM) for 4 hours. Controls samples were analyzed at 4 h following DMSO treatment. For Top1 down-regulation, HCT116 cells were transfected with a siRNA duplex (Qiagen, Valencia, CA) against the sequence AAGGACTCCATCAGATACTAT from the Top1 mRNA. A negative control siRNA duplex was obtained from Qiagen (target DNA sequence: AATTCTCCGAACGTGTCACGT). Cells were seeded in 6-well plates, at a density of 150,000 cells per well 16 hours before transfection. For each sample, 500 pmoles of siRNA were mixed with 250 mL Optimem (Invitrogen) (mix A). Five mL lipofectamine 2000 (Invitrogen) were mixed with 250 mL Optimem and incubated for 5 minutes at room temperature (mix B). After combining mixes A and B, reactions were further incubated for 20 minutes at room temperature before adding the siRNA/lipofectamine complexes in 2 mL culture medium. After 5 hours, the medium was replaced with regular medium and cells were incubated for a further 72 hours.

tag: cell line

tag: cell type

value: colon carcinoma cells

tag: transfection

value: with a Top1 siRNA


title: timepoint 8 hrs; pig 3 Salmonella Cy3 vs pig 3 Mock Cy5

description: slide 033: 8 hours pig 3; Salmonella-fluorescein/Cy3 vs Mock-biotin/Cy5; dye-swap: slide 028


title: HCT116 control siRNA - experiment 2

description: HCT116 cells transfected with a negative control siRNA

scan_protocol: The array work was done by a core facility according to the Affymetrix standard protocol for exon arrays.

value: with a negative control siRNA


title: MCF7 CPT 4 h bis

description:
MCF7 cells treated with 10 uM CPT during 4 h
Solier_D_HuEx-1_0-st-v2.CEL

source_name: cell line - MCF7

label_protocol: The array work was done by a core facility according to the Affymetrix standard protocol for exon arrays.

tag: time point

value: 4 h

value: breast carcinoma cells

tag: agent

value: CPT


title: HCT116 Top1 siRNA - experiment 1


title: Standard Cage-Clean Air 1-1

description: Gene expression in the olfactory bulb of mouse reared in standard cage and then housed in clean air chamber

source_name: Reared in standard cage and housed in clean air

value: olfactory bulb

value: standard cage

value: clean air


title: Pooled RPE/Choroid

description: Pooled from six donors

source_name: RPE/Choroid

value: RPE/Choroid


title: Pooled ONH

description: Pooled from six donors

source_name: Optic nerve head ONH

value: Optic nerve head ONH


title: Pooled Sclera

description: Pooled from six donors

source_name: Sclera

value: Sclera


title: Pooled Retina

description: Pooled from six donors

source_name: Retina

value: Retina


title: Pooled CB

description: Pooled from six donors

source_name: Ciliary Body

value: Ciliary Body


title: Pooled TM

description: Pooled from six donors

source_name: Trabecular Meshwork

value: Trabecular Meshwork


title: HCT116 control siRNA - experiment 1


title: MCF7 CPT 4 h

description:
MCF7 cells treated with 10 uM CPT during 4 h
Solier_C_HuEx-1_0-st-v2.CEL


title: Pooled Iris

description: Pooled from six donors

source_name: Iris

value: Iris


title: MCF7 control DMSO 4 h bis

description:
MCF7 cells treated with 0.1% DMSO during 4 h
Solier_B_HuEx-1_0-st-v2.CEL

value: DMSO


title: Pooled Cornea

description: Pooled from six donors

source_name: Cornea

value: Cornea


title: HCT116 CPT 20 h

description:
HCT116 cells treated with 10 uM CPT during 20 h
Solier_20_HuEx-1_0_st_v2.CEL

value: colon carcinoma cells


title: timepoint 8 hrs; pig 2 Mock Cy3 vs pig 2 Salmonella Cy5

description: slide 117: 8 hours pig 2; Mock-fluorescein/Cy3 vs Salmonella-biotin/Cy5; dye-swap: slide 118

value: pig 2

value: jejunum

value: 8 hours perfusion

value: mock infected

value: Salmonella enterica serovar typhimurium DT104


title: Pooled Lens

description: Pooled from six donors

source_name: Lens

value: Lens


title: HCT116 CPT 15 h

description:
HCT116 cells treated with 10 uM CPT during 15 h
Solier_15_HuEx-1_0_st_v2.CEL

value: CPT


title: MCF7 control DMSO 4 h

description:
MCF7 cells treated with 0.1% DMSO during 4 h
Solier_A_HuEx-1_0-st-v2.CEL

value: 4 h

value: breast carcinoma cells


title: HCT116 CPT 4 h

description:
HCT116 cells treated with 10 uM CPT during 4 h
Solier_4_HuEx-1_0_st_v2.CEL


title: HCT116 CPT 1 h

description:
HCT116 cells treated with 10 uM CPT during 1 h
Solier_1_HuEx-1_0_st_v2.CEL

value: 1 h


title: HCT116 CPT 2 h

description:
HCT116 cells treated with 10 uM CPT during 2 h
Solier_2_HuEx-1_0_st_v2.CEL

value: 2 h


title: HCT116 control DMSO 4 h

description:
HCT116 cells treated with 0.1% DMSO during 4 h
Solier_ctl4_HuEx-1_0_st_v2.CEL


title: HCT116 control DMSO 20 h

description:
HCT116 cells treated with 0.1% DMSO during 20 h
Solier_ctl20_HuEx-1_0_st_v2.CEL


title: DLD-CS vs. DLD-AS_2

city: Gwangju

first: Ho Jin

last: You

address: Seosuk-dong 375

department: Pharmacology

country: South Korea

institute: Chosun University School of Medicine

description: cell line passage #3

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

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

source_name: From ATCC : CCL-221, colon

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Cells were cultured in RPMI-1640 with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin. Cells were maintained in 5% CO2-humidified atmosphere at 37C.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

tag: sample description

value: epithelial, Dukes'type C, colorectal adenocarcinoma

tag: age

value: adult

tag: treatment

value: control shRNA

value: APE(ref-1) shRNA


title: HCT116 CPT 20 h

description: HCT116 cells treated with 10 μM CPT during 20 h

hyb_protocol: The array work was done by a core facility according to the Agilent's standard protocol for miRNA arrays.

scan_protocol: Agilent Technologies Scanner G2505C  miRNA_107_Sep09

data_processing: TotalGeneSignal values were used from the Agilent results files.  The Agilent software does background correction and summarizes several probe values into the total gene signal.  Values are log2 transformed.  No cross chip normalizaiton was performed.  Note: 4H Control showed a different distribution than other samples so we used just the 20H control.

source_name: HCT116 cells

growth_protocol: Human HCT116 cell line was obtained from ATCC (Rockville, MD) and grown in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Gemini Bio-products, West Sacramento, CA) at 37 degrees Celsius in 95% air and 5% CO2.

treatment_protocol: HCT116 cells were treated with CPT for 1, 2, 4, 15 and 20 hours. Controls samples were analyzed at 4 and 20 h following DMSO treatment (0.1%; the solvent used to dissolve CPT).


title: HCT116 CPT 15 h

description: HCT116 cells treated with 10 μM CPT during 15 h

label_protocol: The array work was done by a core facility according to the Agilent's standard protocol for miRNA arrays.


title: M-BMM-2

city: Birmingham

first: Gang

last: Liu

state: Alabama

address: 901 19TH ST S

department: Medicine

institute: University of Alabama at Birmingham

description:
Liu-4
Liu-4
Biological replicate 2 of 2. M-BMM cells
1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the mercury LNA™ microRNA Array 6th gen (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 16.0. The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing: The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm. Spots on the array annotated for human and/or rats were filtered out, and only the ~1000 spots which is annotated for mouse and related viruses were preserved.

source_name: M-CSF-induced BMM

label_protocol: 750 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: Mouse bone marrow-derived macrophages (BMM) were derived from bone marrow cells of C57BL/6 mice, and cultured in DMEM media containing 10% FBS and 20 ng/ml GM-CSF or 50 ng/ml M-CSF, respectively.

extract_protocol: Total RNA extracted using Qiagen RNAeasy kit following manufacturer's instructions

treatment_protocol: To established GM-CSF-induced BMM (GM-BMM) and M-CSF-induced BMM (M-BMM), BMM were cultured in DMEM media containing 10% FBS and 20 ng/ml GM-CSF or 50 ng/ml M-CSF for 5 days.

tag: strain background

value: bone marrow-derived macrophages (BMM)

tag: induced with

value: 50 ng/ml M-CSF for 5 days

source_name: mouse bone marrow-derived macrophages (BMM)

tag: sample type

value: common reference; pooled total RNA of equal amount of the 4 samples


title: M-BMM-1

description:
Liu-3
Liu-3
Biological replicate 1 of 2. M-BMM cells
1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.


title: GM-BMM-1

description:
Liu-1
Liu-1
Biological replicate 1 of 2.GM-BMM cells
1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.

source_name: GM-CSF-induced BMM

value: 20 ng/ml GM-CSF for 5 days


title: HCT116 CPT 4 h

description: HCT116 cells treated with 10 μM CPT during 4 h

value: colon carcinoma cells


title: SW480-PC vs. SW480-APE_2

description: cell line passage #3

source_name: From ATCC : CCL-228, colon

value: epithelial, Dukes'type B, colorectal adenocarcinoma

value: 50 years


title: DLD-CS vs. DLD-AS_1

description: cell line passage #3


title: GM-BMM-2

description:
Liu-2
Liu-2
Biological replicate 2 of 2.GM-BMM cells
1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.


title: HCT116 CPT 2 h

description: HCT116 cells treated with 10 μM CPT during 2 h


title: HCT116 CPT 1 h

description: HCT116 cells treated with 10 μM CPT during 1 h


title: non-AD_HI, biological rep8

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were imported into Affymetrix Expression Console Software, and CHP files were generated.

source_name: Hippocampus of of non-AD brain

label_protocol: The Ambion WT Expression Kit and the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) were used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol: We examined postmortem human brains donated for the Hisayama study.

extract_protocol: Total RNA was isolated using a combination of Isogen (Nippon Gene) and the RNeasy Mini Kit (Qiagen), according to the manufacturers’ instructions.

treatment_protocol: During autopsy dissection, parts of the frontal cortex, temporal cortex and hippocampus were cut out from each brain, and preserved at –80°C until RNA preparation.

tag: tissue

value: Hippocampus

tag: Sex

value: M


title: HCT116 control DMSO 20 h

description: HCT116 cells treated with 0.1% DMSO during 20 h

value: DMSO


title: non-AD_HI, biological rep6

value: F


title: non-AD_HI, biological rep3


title: non-AD_HI, biological rep9


title: non-AD_HI, biological rep4


title: non-AD_HI, biological rep7


title: HCT116 control DMSO 4 h

description: HCT116 cells treated with 0.1% DMSO during 4 h

value: 4 h


title: non-AD_HI, biological rep5


title: non-AD_HI, biological rep2


title: DMSO-treated cells, rep 2

city: Illkirch

first: Susan

last: Chan

address: 1, rue Laurent Fries

country: France

institute: IGBMC

hyb_protocol: 10 μg of cRNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse 430 2.0 arrays (Affymetrix)

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm.

data_processing: CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor with default settings to calculate probe set signal intensities

source_name: DMSO-treated cells, rep 2

label_protocol: Biotinylated cRNA targets were prepared according to Affymetrix recommendations in  GeneChip® Expression Analysis Technical Manual  (P/N 702232 Rev.2) starting from 2.0-2.5 µg of total RNA  in a one cycle target labeling assay.

growth_protocol: Cells were grown in RPMI1640, 10% FCS, 1mM sodium pyruvate, 2mM L-glutamine and 1% antibiotics.

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy kit

treatment_protocol: Cells were treated with 5mM of the gamma-secretase inhibitor MRK003 (Merck) for 36h.

value: T29 thymic lymphoma cell line


title: non-AD_HI, biological rep1


title: GSI treated cells, rep2

source_name: GSI treated cells, rep2


title: AD_HI, biological rep6

source_name: Hippocampus of of AD brain


title: PCN_control shRNA_rep3

city: Nagoya

first: Shinsuke

last: Ishigaki

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Neurology

institute: Nagoya University School of Medicine

description: RMA expression value derived from Expression Console software; all-exon analysis

hyb_protocol: Samples were hybridized with GeneChip mouse exon 1.0 ST Arrays (Affymetrix) and scanned accoding to the manufacture's protocol.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip 3000 7G

data_processing:
The data were background corrected and normalized using the robust multiarray average (RMA) procedure implemented in the Affymetrix Expression Console software.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dtl.mm9.full.ps

source_name: primary cortical neurons, control shRNA

label_protocol: 100ng of total RNA were used to generate labeled cDNA. Biotinylated DNA probes were prepared using Affymetrix WT Expression kit for Affymetrix Whole Transcript Sense Expression arrays and Affymetrix geneChip WT Terminal Labeling kit according to the manufacture's protocol.

growth_protocol: Mouse fetal brain was taken from C57BL/6 mouse embryos at E15. After removing meninges cortical tissue was dissociated into a single-cell suspension by Sumilon dissociation solution (Sumitomo Bakelite, Tokyo Japan). Cells were plated at a density of 1.5 x 106 cells in a 60 mm-well culture plate with the medium containing 0.5x Sumilon nerve-culture medium (Sumitomo Bakelite), 0.5x Neurobasal medium, 1% FBS, 0.5x B27 supplements (Invitrogen), 0.5x Glutamax, 5 µg/ml of BDNF, 5 µg/ml of CNTF, and 0.5% Pen-Strep. A day after plating (day 2), neurons were supplemented with 10 ng/µl of AraC and incubated overnight.

extract_protocol: Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) followed by DnaseI (Qiagen) treatment.

treatment_protocol: On day 5, neurons were infected with 2 x 1010 copies/well (1.5 x 107 copies/µl) of lentivirus expressing shRNA against mouse Tdp-43 (shTdp-43-1 or shTdp-43-2) or control (shCont). After 4 hr of infection, the virus media was removed. Neurons were then cultured for 6 additional days, and were harvested on day 11 followed by RNA extraction and cDNA synthesis.

tag: strain

tag: developmental stage

value: embryo

value: primary cortical neurons

tag: genotype/variation

value: control


title: AD_HI, biological rep7


title: AD_HI, biological rep5


title: DMSO-treated cells, rep 1

source_name: DMSO-treated cells, rep 1


title: GSI treated cells, rep1

source_name: GSI treated cells, rep1


title: PCN_shRNA Tdp-43-2_rep3

source_name: primary cortical neurons, shRNA Tdp-43-2

value: Tdp-43-2 knockdown


title: PCN_shRNA Tdp-43-2_rep2


title: Ikf/f CD4-Cre+ sample 2 (mouse 69)

hyb_protocol: 10 μg of cRNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse 430 2.0 arrays (Affymetrix).

data_processing: CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor with default settings to calculate probe set signal intensities .

source_name: Ikf/f CD4-Cre+ sample 2 (mouse 69)

label_protocol: Biotinylated cRNA targets were prepared according to Affymetrix recommendations in  GeneChip Expression Analysis Technical Manual  (P/N 702232 Rev.2) starting from [100 ng (A810) ; 50 ng (A1052) ; 15-100 ng (A1031)] of total RNA  in a two cycle target labeling assay.

tag: genotype

value: Ikf/f CD4-Cre+


title: non-AD_TC, biological rep19

source_name: Temporal cortex of non-AD brain

value: Temporal cortex


title: PCN_control shRNA_rep2


title: PCN_shRNA Tdp-43-1_rep3

source_name: primary cortical neurons, shRNA Tdp-43-1

value: Tdp-43-1 knockdown


title: SW480-PC vs. SW480-APE_1

description: cell line passage #3

tag: cell line


title: PCN_shRNA Tdp-43-2_rep1

tag: cell type


title: non-AD_TC, biological rep14


title: Ikf/f CD4-Cre- sample 1 (mouse 52)

source_name: Ikf/f CD4-Cre- sample 1 (mouse 52)

value: Ikf/f CD4-Cre-


title: AD_HI, biological rep1


title: non-AD_TC, biological rep13


title: Ikf/f CD4-Cre+ sample 1 (mouse 53)

source_name: Ikf/f CD4-Cre+ sample 1 (mouse 53)


title: Ikf/f CD4-Cre- sample 2 (mouse 57)

source_name: Ikf/f CD4-Cre- sample 2 (mouse 57)


title: AD_HI, biological rep2


title: PCN_shRNA Tdp-43-1_rep1


title: IkL/L DN3 cells, GSI treated, rep2

data_processing: CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor with default settings to calculate probe set signal intensities.

source_name: IkL/L DN3 cells, GSI treated, rep2

growth_protocol: Lineage-negative thymocytes were isolated by magnetic bead mediated depletion and cultured on OP9 DL1 cells in RPMI1640, 10% FCS, 1mM sodium pyruvate, 2mM L-glutamine and 1% antibiotics.

extract_protocol: DN3 cells (Lin-CD44-CD25+) were sorted from the culture. Total RNA was extracted with the Qiagen RNAeasy kit.

treatment_protocol: Cells were treated with 5mM of the gamma secretase inhibitor MRK-003 or DMSO (vehicle) for 16h.

value: IkL/L

value: DN3 cells

value: gamma secretase inhibitor MRK-003


title: non-AD_TC, biological rep15


title: PCN_shRNA Tdp-43-1_rep2


title: non-AD_TC, biological rep12


title: non-AD_TC, biological rep9


title: IkL/L DN3 cells, GSI treated, rep1

source_name: IkL/L DN3 cells, GSI treated, rep1


title: non-AD_TC, biological rep11


title: non-AD_TC, biological rep10


title: AD_HI, biological rep3

value: Hippocampus


title: IkL/L DN3 cells, DMSO treated, rep2

source_name: IkL/L DN3 cells, DMSO treated, rep2


title: PCN_control shRNA_rep1


title: IkL/L DN3 cells, DMSO treated, rep1

source_name: IkL/L DN3 cells, DMSO treated, rep1


title: non-AD_TC, biological rep7


title: non-AD_TC, biological rep8

value: M


title: AD_HI, biological rep4


title: non-AD_TC, biological rep1


title: non-AD_TC, biological rep6


title: non-AD_TC, biological rep2


title: non-AD_TC, biological rep3


title: AD_TC, biological rep10

source_name: Temporal cortex of AD brain


title: AD_TC, biological rep8


title: non-AD_TC, biological rep5


title: AD_TC, biological rep9


title: non-AD_TC, biological rep4


title: AD_TC, biological rep7


title: AD_TC, biological rep6


title: WT DN3 cells, GSI treated, rep1

source_name: WT DN3 cells, GSI treated, rep1

value: WT


title: WT DN3 cells, GSI treated, rep2

source_name: WT DN3 cells, GSI treated, rep2


title: AD_TC, biological rep3

value: F


title: AD_TC, biological rep1


title: DP cells rep 2

description: sorted cells from mouse thymus

source_name: DP cells rep 2

label_protocol: Biotinylated cRNA targets were prepared according to Affymetrix recommendations in  GeneChip Expression Analysis Technical Manual  (P/N 702232 Rev.2) starting from [100 ng (A810) ; 50 ng (A1052) ; 15-100 ng (A1031)] of total RNA  in a two cycle target labeling assay

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy micro  kit

value: thymus

value: DP cells


title: WT DN3 cells, DMSO treated, rep1

source_name: WT DN3 cells, DMSO treated, rep1

value: DMSO


title: DN4 cells rep 2

description: sorted cells from mouse thymus

source_name: DN4 cells rep 2

value: DN4 cells


title: AD_TC, biological rep2


title: AD_TC, biological rep4


title: DN3 cells rep 1

description: sorted cells from mouse thymus

source_name: DN3 cells rep 1


title: DN4 cells rep 1

description: sorted cells from mouse thymus

source_name: DN4 cells rep 1


title: non-AD_FC, biological rep14

source_name: Frontal cortex of non-AD brain

value: Frontal cortex


title: AD_TC, biological rep5


title: non-AD_FC, biological rep15


title: non-AD_FC, biological rep13


title: DN3 cells rep 2

description: sorted cells from mouse thymus

source_name: DN3 cells rep 2


title: WT DN3 cells, DMSO treated, rep2

source_name: WT DN3 cells, DMSO treated, rep2


title: DP cells rep 1

description: sorted cells from mouse thymus

source_name: DP cells rep 1


title: non-AD_FC, biological rep16


title: non-AD_FC, biological rep10


title: WT DP cells rep 2

description: sorted cells from mouse thymus

source_name: WT DP cells rep 2


title: non-AD_FC, biological rep11


title: non-AD_FC, biological rep9


title: non-AD_FC, biological rep7


title: WT DP cells rep 1

description: sorted cells from mouse thymus

source_name: WT DP cells rep 1


title: non-AD_FC, biological rep8


title: non-AD_FC, biological rep5


title: WT DN4 cells rep 2

description: sorted cells from mouse thymus

source_name: WT DN4 cells rep 2


title: WT DN3 cells rep 1

description: sorted cells from mouse thymus

source_name: WT DN3 cells rep 1


title: MigR1-MLER transduced, 4OHT treated rep 2

label_protocol: Biotinylated cRNA targets were prepared according to Affymetrix recommendations in  GeneChip® Expression Analysis Technical Manual  (P/N 702232 Rev.2) starting from 2.0-2.5 µg of total RNA  in a one cycle target labeling assay

treatment_protocol: Cells were treated with 100 nM 4OHT or ethanol for 24h.

value: T29 thymic lymphoma cell line


title: WT DN4 cells rep 1

description: sorted cells from mouse thymus

source_name: WT DN4 cells rep 1


title: non-AD_FC, biological rep3


title: non-AD_FC, biological rep6


title: AD_FC, biological rep14

source_name: Frontal cortex of AD brain


title: AD_FC, biological rep15


title: WT DN3 cells rep 2

description: sorted cells from mouse thymus

source_name: WT DN3 cells rep 2


title: non-AD_FC, biological rep2


title: non-AD_FC, biological rep12


title: non-AD_FC, biological rep1


title: MigR1-MLER transduced, ethanol treated rep 2


title: AD_FC, biological rep13


title: AD_FC, biological rep12


title: non-AD_FC, biological rep4


title: AD_FC, biological rep11


title: AD_FC, biological rep10


title: MigR1-MLER transduced, ethanol treated rep 1


title: AD_FC, biological rep9


title: AD_FC, biological rep8


title: MigR1-MLER transduced, 4OHT treated rep 1


title: AD_FC, biological rep5


title: AD_FC, biological rep4


title: AD_FC, biological rep6


title: MigR1-Ik1ER transduced, ethanol treated rep 2

growth_protocol: Clles were grown in RPMI1640, 10% FCS, 1mM sodium pyruvate, 2mM L-glutamine and 1% antibiotics.

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy kit.


title: MigR1-Ik1ER transduced, 4OHT treated rep 1


title: MigR1-Ik1ER transduced, ethanol treated rep 1


title: MigR1-Ik1ER transduced, 4OHT treated rep 2


title: AD_FC, biological rep7


title: M_lung_BJ501_5dpi_sample3

city: Beijing

first: Peng

last: Li

address: Dongda street 20# Fengtai District

department: Department of Infectious Disease Control

country: China

institute: Institute of Disease Control and Prevention

hyb_protocol: Cy3-labelled RNA was dried on the medium-high heat setting with a vacuum concentrator according to the manufacture's protocol. On completion of sample dryness, 22.5 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 20 hours at 55°C in a rotating Agilent hybridization oven at 20 rpm.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C 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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.The extracted data were then normalized with Agilent GeneSpring 12.0 by three main steps. First,a filtering step is done wherein both flag (gIsGeneDetected column) and error (gTotalProbeError column) is taken into account. Only those rows are used that have a flag value of 1. For each miRNA, if all flags are 0 then the signal value is taken as 0.1. Or GeneSpring uses only those rows for summarization which have value of 1. Then if the signal value passes the filter(greater than 3 times the error value), it is used and assigned with a value of 0 for error. Second,the multiple probes that map to a given systematic name are first summed up. The signal value is computed as the SUM of all values and not average. Summarization is based on the systematic name as explained above and is done before thresholding of signal values. Last,the data was then normalizes to 90th percentile with Percnetile Shift algorithms.

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by Qiagen RNAeasy Mini Kit(QIAGEN 217004, Valencia, CA).  Dye incorporation and RNA yield were checked with the NanoDrop ND-1000 Spectrophotometer (Thermo).

extract_protocol: Whole mouse lung tissues were homogenized in QIAzol lysis regant (Qigen). Total RNA was extracted from mouse lung using miRvana miRNA isolation kit (Ambion) according to the manufacturer’s protocol. The concentration of RNA was determined by a Nanodrop ND-1000 Spectrophotometer (Thermo)

treatment_protocol: Specific pathogen-free 6- to 8-week-old male BALB/c mice were intranasally inoculated with 10^4 TCID50 (25 µl) of BJ501 or PR8 virus respectively. In addition, a normal control group were set up and given i.n. phosphate buffered saline (PBS)

value: BALB/c

tag: gender

value: male

value: 6- to 8-weeks

tag: infected with

value: influenza virus BJ501

value: 5 dpi

value: whole lung


title: AD_FC, biological rep2


title: AD_FC, biological rep3


title: M_lung_PR8_5dpi_sample4

value: mouse-adapted influenza virus A/Puerto Rico/8/34 (H1N1)(PR8)

tag: time point


title: M_lung_PR8_5dpi_sample5


title: MigR1 transduced, ethanol treated rep 2

source_name: MigR1 transduced, ethanol treated rep 2


title: MigR1 transduced, 4OHT treated rep 2

source_name: MigR1 transduced, 4OHT treated rep 2


title: MigR1 transduced, 4OHT treated rep1

source_name: MigR1 transduced, 4OHT treated rep1


title: M_lung_BJ501_2dpi_sample4

value: 2 dpi


title: M_lung_PR8_5dpi_sample3


title: M_lung_BJ501_2dpi_sample5


title: M_lung_BJ501_2dpi_sample1


title: M_lung_BJ501_5dpi_sample2


title: MigR1 transduced, ethanol treated rep 1

source_name: MigR1 transduced, ethanol treated rep 1


title: M_lung_PR8_2dpi_sample5


title: NestinCreERT10;Tlx f/f; N-Tva CRE+, 6103

city: Heidelberg

first: Hai-Kun

country: Germany

institute: Deutsches Krebsforschungszentrum DKFZ

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol using an iScan array scanner.

data_processing: Data extraction was done for all beads individually, and outliers were removed when > 2.5 MAD (median absolute deviation). All remaining data points were used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated. The data was quantile normalized using R (function normalize.quantiles from library preprocessCore).

source_name: Mouse brain glioma, Tlx knockout

label_protocol: Biotinylated cRNA were prepared with the Illumina® Total Prep™ RNA Amplification Kit (Life Technologies) for Illumina arrays.

extract_protocol:
The mouse brain gliomas were excised from the sacrificed animal and put into a suitably sized vessel containing RNAlater. Four hours later, the glioma tissues were put into Trizol. The tissues were disrupted and homogenized by using a rotor-stator homogenizer, until it became a uniformly homogeneous lysate. Centrifuge the lysate for 3 min at 12000 rpm, carefully remove the supernatant by pipetting and transfer it to a new microcentrifuge tube, use only this supernatant (lysate) in subsequent steps.
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyzer and NanoDrop.

treatment_protocol: Brain gliomas were initiated from the Nestin-CreERT2;Tlx flox/flox;Nestin-Tva transgenic mouse line. After 2.5 weeks, when the brain gliomas were fully developed, tamoxifen was administered through intraperitoneal injection. Tlx was knocked-out from the Cre-expressing littermates, but the littermates without Cre expression maintained intact Tlx function.

tag: strain/background

value: Nestin-CreERT10;Tlx f/f; N-Tva CRE+

value: 60 days

value: brain glioma


title: AD_FC, biological rep1

tag: age

value: M


title: M_lung_PR8_2dpi_sample3


title: DN4 cells sorted from mouse n°137 (Cre-)

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy micro kit

treatment_protocol: Ikf/f Rosa26-CreERT2+ mice after daily intraperitoneal injections of tamoxifen (50 mg/kg weight of mouse, dissolved in sunflower oil) for 4 days. Mice were analyzed 24h after the last injection.


title: M_lung_PR8_2dpi_sample2


title: NestinCreERT9;Tlx f/f; N-Tva CRE+, 5611

value: Nestin-CreERT9;Tlx f/f; N-Tva CRE+

value: 48 days


title: NestinCreERT12;Tlx f/f; N-Tva CRE+, 5631

value: Nestin-CreERT12;Tlx f/f; N-Tva CRE+

value: 79 days


title: NestinCreERT3;Tlx f/f; N-Tva CRE-, 5622

source_name: Mouse brain glioma, intact Tlx

value: Nestin-CreERT3;Tlx f/f; N-Tva CRE-

value: 42 days


title: NestinCreERT7;Tlx f/f; N-Tva CRE-, 080312

value: Nestin-CreERT7;Tlx f/f; N-Tva CRE-

value: 46 days


title: NestinCreERT8;Tlx f/f; N-Tva CRE+, 6105

value: Nestin-CreERT8;Tlx f/f; N-Tva CRE+

value: 58 days


title: NestinCreERT6;Tlx f/f; N-Tva CRE-, 13.03_2

value: Nestin-CreERT6;Tlx f/f; N-Tva CRE-

value: 51 days


title: NestinCreERT5;Tlx f/f; N-Tva CRE-, 100312

value: Nestin-CreERT5;Tlx f/f; N-Tva CRE-

value: 50 days


title: M_lung_C_uninfected_sample4

value: BALB/c

value: male

value: 6- to 8-weeks

value: none (uninfected control)

value: whole lung


title: NestinCreERT2;Tlx f/f; N-Tva CRE-, 5619

value: Nestin-CreERT2;Tlx f/f; N-Tva CRE-

value: brain glioma


title: DN4 cells sorted from mouse n°135 (Cre+)


title: DN4 cells sorted from mouse n°131 (Cre-)


title: NestinCreERT4;Tlx f/f; N-Tva CRE-, 5943

value: Nestin-CreERT4;Tlx f/f; N-Tva CRE-

value: 38 days


title: M_lung_C_uninfected_sample3


title: DN4 cells sorted from mouse n°129 (Cre+)


title: M_lung_C_uninfected_sample1


title: non-Tg_1, biological rep2

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

source_name: Hippocampus of  non-Tg mouse

growth_protocol: Each mouse was maintained in SPF condition and sacrificed at 14 months of age.

treatment_protocol: Brains were removed from each mouse under pentobarbital anesthesia (i.p), with perfusion of 40 ml of saline via the left ventricle. Hippocampi were isolated and preserved at –80°C until RNA preparation.

value: Hippocampus

value: non-Tg

value: 14 months of age


title: non-Tg_1, biological rep3


title: 3xTg-AD-h, biological rep1

source_name: Hippocampus of 3xTg-hetero mouse


title: 3xTg-AD-h, biological rep2


title: 3xTg-AD-H, biological rep1

source_name: Hippocampus of 3xTg-Homo mouse


title: 3xTg-AD-H, biological rep2


title: 3xTg-AD-H, biological rep3


title: 3xTg-AD-h, biological rep3


title: non-Tg_1, biological rep1


title: Adrenal_SHR_3w-biological rep2

status: Public on Apr 16 2013

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: adrenal glands  derived from 3 week-old SHR rat strain

hyb_protocol: Before hybridization, 1650 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction, LOWESS normalization, and dye-normalization .

organism: Rattus norvegicus

source_name: adrenal glands derived from 3w SHR rat strain

label_protocol: 200 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 200 ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNAs were extracted from adrenal glands stored in RNA later (Ambion), derived from WKY, SHR and SHRSP rats using miRNeasy extraction kit (Qiagen) following manufacturer's instructions.

treatment_protocol: no teatment


title: Adrenal_SHRSP_6w-biological rep3

description: adrenal glands  derived from 6 week-old SHRSP rat strain

source_name: adrenal glands derived from 6w SHRSP rat strain


title: Adrenal_WKY_3w-biological rep3

description: adrenal glands  derived from 3 week-old WKY rat strain

source_name: adrenal glands derived from 3w WKY rat strain


title: Adrenal_WKY_3w-biological rep1


title: Adrenal_WKY_6w-biological rep3

description: adrenal glands  derived from 6 week-old WKY rat strain

source_name: adrenal glands derived from 6w WKY rat strain


title: Adrenal_SHR_3w-biological rep1


title: Adrenal_SHR_6w-biological rep2

description: adrenal glands  derived from 6 week-old SHR rat strain

source_name: adrenal glands derived from 6w SHR rat strain


title: Adrenal_SHRSP_6w-biological rep1


title: Adrenal_WKY_6w-biological rep2


title: Adrenal_SHR_6w-biological rep3


title: Adrenal_SHR_3w-biological rep3


title: Adrenal_SHRSP_3w-biological rep3

description: adrenal glands  derived from 3 week-old SHRSP rat strain

source_name: adrenal glands derived from 3w SHRSP rat strain


title: Adrenal_WKY_3w-biological rep2


title: Adrenal_SHR_6w-biological rep1


title: Adrenal_SHRSP_3w-biological rep2


title: Adrenal_SHRSP_6w-biological rep2


title: Adrenal_WKY_6w-biological rep1


title: Adrenal_SHRSP_3w-biological rep1


title: ES derived Flk-1+Hoxb6-Venus+ cells, rep.2

city: Kobe

first: Hiroshi

last: Kataoka

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Stem Cell Biology

institute: Riken Center for Developmental Biology

hyb_protocol: We used Gene Expression Hybridization Kit, Gene Expression Wash Buffers Pack and followed manufacturer's protocol.

scan_protocol: We used Agilent Microarray Scanner, and followed manufacturer's protocol.

data_processing: We used Agilent Feature Extraction for quantification. Normalization was performed with trimmed mean.

source_name: mouse EB5 ES cells introduced Hoxb6-Venus reporter. Indicated fraction of differentiated ES cells were purified by cell sorting.

label_protocol: We used Agilent Low Input Quick Amp Labeling Kit, and followed manufacturer's protocol.

growth_protocol: ES cells were differentiated on OP9 feeder cells for 6 days.

extract_protocol: Total RNA was purified from sorted cells using micro-elute RNA purification kit from Qiagen.

treatment_protocol: Differentiated ES cells were sorted using Hoxb6 reporter and Flk-1 antibody staining.

value: Flk-1+Hoxb6-Venus+ fraction of day6 differentiated ES cells


title: ES derived Flk-1+Hoxb6-RFP+ cells,rep2

source_name: mouse EB5 ES cells introduced Hoxb6-RFP reporter. Indicated fraction of differentiated ES cells were purified by cell sorting.

value: Flk-1+Hoxb6-RFP+ fraction of day6 differentiated ES cells


title: NestinCreERT13;Tlx f/f; N-Tva CRE+, 5616

value: Nestin-CreERT13;Tlx f/f; N-Tva CRE+

value: 63 days


title: NestinCreERT11;Tlx f/f; N-Tva CRE+, 6102

value: Nestin-CreERT11;Tlx f/f; N-Tva CRE+

value: 65 days


title: ES derived Flk-1+Hoxb6-Venus- cells, rep.1

value: Flk-1+Hoxb6-Venus- fraction of day6 differentiated ES cells


title: ES derived Flk-1+Hoxb6-RFP- cells,rep2

value: Flk-1+Hoxb6-RFP- fraction of day6 differentiated ES cells


title: ES derived Flk-1+Hoxb6-RFP- cells,rep1


title: ES derived Flk-1+Hoxb6-Venus+ cells, rep.1


title: ES derived Flk-1+Hoxb6-RFP+ cells,rep1


title: M_lung_BJ501_5dpi_sample4

value: BALB/c

value: male

value: 6- to 8-weeks

value: influenza virus BJ501

value: 5 dpi


title: ES derived Flk-1+Hoxb6-Venus- cells, rep.2


title: Retina_SH-80_7days_rep2

city: Seoul

first: Jeong Hun

last: Kim

address: 101, Daehak-ro, Jongno-gu

institute: Seoul National University

source_name: retina, 7 days

growth_protocol: We intravitreally injected 1 μM of PBS, SH-42, or SH-80 into the right eyes of C57BL/6 male mice. One week later, the mice were sacrificed and the eyes were enucleated.

treatment_protocol: Retinal tissues were prepared from the enucleated eyes. Four retinal tissues were pooled into 1 test tube.

value: retina

value: adult

tag: treatment

value: control


title: Insulin Sensitive IS 0137EG

city: Chicago

first: Eric

last: Gamazon

state: IL

address: KCBD 3220 900 E 57th Street

institute: University of Chicago

hyb_protocol: We fragmented 1 µg of purified cRNA to uniform size and hybridized to Human Whole Genome 4x44k arrays (Agilent Technologies, Santa Clara, CA, USA) at 37° C for 18 hrs,

scan_protocol: Scanned with a G2565 Microarray Scanner (Agilent Technologies)

data_processing: Arrays were processed and background corrected with default settings of the Agilent Feature Extraction software v.9.5.3.1 (Agilent Technologies). Raw intensity data from each gene were quantile normalized to the 75th percentile intensity of each array. Only transcripts with values greater than background intensity in all samples were included for analysis in the current study.

source_name: adipose

label_protocol: RNA was extracted, and labeled cRNA prepared by linear amplification of the poly(A)+ RNA population within the total RNA sample.  Total RNA (1 µg) was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence. After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: adipose

tag: phenotype

value: Insulin Sensitive IS


title: Insulin Sensitive IS 0111CT


title: Insulin Resistant IR 0120AB

value: Insulin Resistant IR


title: Retina_SH-42_7days_rep3


title: Insulin Resistant IR 0206127CU


title: Insulin Sensitive IS 0131DW


title: Insulin Sensitive IS 0106KJ


title: Insulin Resistant IR 0117KT


title: Retina_SH-80_7days_rep3


title: Insulin Sensitive IS 059SV


title: Insulin Resistant IR 098DE


title: Insulin Resistant IR 072FA


title: Insulin Resistant IR 0206128AS


title: Insulin Sensitive IS 0116GJ


title: Insulin Resistant IR 502007JB


title: Insulin Resistant IR 0206143VH


title: Retina_SH-42_7days_rep1


title: Insulin Resistant IR 0156YT


title: Retina_SH-80_7days_rep1


title: Insulin Resistant IR 0502004AJ


title: Insulin Sensitive IS 0126TW


title: Retina_SH-42_7days_rep2


title: Insulin Resistant IR 0152MH


title: Insulin Sensitive IS M033JK


title: Insulin Sensitive IS M049PM


title: Insulin Resistant IR M032AF


title: Insulin Sensitive IS M019AS


title: Insulin Sensitive IS 099KS


title: Insulin Resistant IR GP08009


title: Insulin Sensitive IS GP07056


title: Insulin Resistant IR GP07049


title: Insulin Resistant IR GP07054


title: Insulin Sensitive IS GP07042


title: Insulin Resistant IR GP07047


title: TCDD treated Hepa1c1c7 vs. TCDD plus blebbistatin

city: Hirosaki

first: Hideaki

last: Kikuchi

address: 3 Bunkyo-cho

department: Faculty of Agriculture and Life Science

institute: Hirossaki University

description: Hepa1c1c7 cells were treated with (-)-blebbistatin (40 uM) for 1 day and then TCDD (4 nM) plus blebbistatin for 6 h.

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

scan_protocol: Scanned on an Agilent Technologies Microarray scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: Hepa1c1c7 cells treated with TCDD

label_protocol: 200 ng of total RNA were primed with 1.8 µl T7 Promoter Primer at 65°C for 5 min, then reversed transcribed at 40°C for 2 h in the presence of 1.2 uL AffinityScript, and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3 or Cy5 (Agilent Technologies).

growth_protocol: Hepa1c1c7 cells were cultured in DMEM medium containing 0.1 U/L penicillin, 0.1 g/L streptomycin and 5% fetal bovine albumin.

extract_protocol: Total RNA extracted using Rneasy Kit (QIAGEN) following manufacturer's instructions.

value: Hepa1c1c7 (ATCC:CRL-2026)

tag: days after passage

value: 4 days after passage

value: liver, carcinoma

value: TCDD

source_name: Hepa1c1c7 treated with TCDD plus blebbistatin

value: TCDD plus blebbistatin


title: Insulin Resistant IR GP07041


title: Insulin Sensitive IS GP07025


title: Insulin Sensitive IS GP07017


title: Replication timing of L1210 cell line, replicate 2

city: Tallahassee

first: David

middle: M.

last: Gilbert

state: Florida

address: 319 Stadium Drive

institute: Florida State University

description: Submitted as of 3-28-13

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (34 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 2.5 kb (MEL, CH12; GPL10989) or 5.8 kb (L1210; GPL9156) across the mouse genome.

scan_protocol: NimbleGen MS200 microarray scanner (Roche NimbleGen, Inc.) and MS200 data collection software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were differentially labeled were loess-normalized to remove signal intensity-dependent bias, then scaled to a reference data set to have the same median absolute deviation (limma package, R/Bioconductor). The early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using the loess function in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245] and Ryba et al [Nature Protocols (2011) 6: 870–895]

source_name: Early-replicating DNA of L1210 cell line

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245] and Ryba et al [Nature Protocols (2011) 6: 870–895]

value: F

source_name: Late-replicating DNA of L1210 cell line


title: Insulin Resistant IR GP07040


title: KTaj-NSM-SQTP_100-1a

city: Baltimore

first: Jonathan

last: Pevsner

state: MD

address: 707 N. Broadway

department: Neurology

institute: Kennedy Krieger Institute

hyb_protocol: The hybridization cocktail was fragmented at 65oC for 30 min

scan_protocol: Scanning was performed according to the Affymetrix protocol at the Microarray Core Facility, Johns Hopkins University.

data_processing: Data analysis was performed using Partek Genomics Suite (version 6.5).

source_name: Corpus striatum

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

extract_protocol: Frontal cortex and striatum were dissected and total RNA was extracted using an Rneasy Mini Kit (Qiagen).

treatment_protocol: Male CD-1 mice were administered vehicle (0.5% methycellulose twice a day), quetiapine (10 or 100 mg/kg twice a day) or haloperidol (0.32 or 1 mg/kg twice a day) for 28 days.

tag: region

value: Corpus striatum

value: quetiapine

tag: dose


title: Insulin Sensitive IS GP07019

tag: tissue


title: Suspension arrested fibroblasts (reference) and suspenison-arrested Myoblasts (test) rep1

city: SAN ANTONIO

first: PRETHISH

last: SREENIVAS

state: TX

address: 8403 Floyd Curl Dr

department: GCCRI

institute: UTHSCSA

description:
C2C12 FS48 Vs M S48 Rep 1
Expression profile of differentially expressed genes in suspension arreseted myoblasts

hyb_protocol: Purified Cy3,Cy5 Labelled cDNA was incubated on the NIA15K5  chip at 42 degree celsius for 16hr.washed with 1XSSC+0.2%SDS for 5 min then second wash with 0.1XSSC+0.2%SDS for 5 min and third wash with 0.1XSSC for 5 min and dried the chip by spinning briefly.

scan_protocol: Scanned using  Molecular Dynamics scanner using excitation wavelengths of 543nm and 663nm.

data_processing: LOWESS normalized, TIGR MIDAS, background subtracted VALUE data obtained from log2 of processed Experimental signal/processed reference signal.

label_protocol: 20 micrograms of RNA is taken for labelling with Cy3/Cy5 dyes. Reverse transcription was performed to make cDNA (1hr 30 min at 42 degrees celsius using SuperScript II from Invitrogen). Unincorporated nucleotides were removed using Millipore Spin columns.

growth_protocol: Grown in Dulbecco's modified Eagle medium supplemented with 20% Fetal calf serum

extract_protocol: RNA was isolated using Trizol Invitrogen.

treatment_protocol: Synchronized cells in G0 and reactivated to enter cell cycle by replating and grown for 24hrs to get synchronized S phase cells

value: C2C12 cells suspended in semi-solid media

source_name: NIH 3T3_suspension arrested fibroblasts (F_S48)

value: NIH 3T3

value: NIH3T3 suspeneded in semi-solid media


title: KTaj-NSM-SQTP_10-1a

value: male

tag: strain


title: KTaj-NSM-SQTP_100-2a


title: Insulin Resistant IR GP07003


title: Insulin Sensitive IS GP06096


title: Insulin Resistant IR GP06075


title: Insulin Sensitive IS GP06097


title: Insulin Resistant IR GP07048


title: Replication timing of L1210 cell line, replicate 1

description: Submitted as of 3-28-13

tag: Sex


title: Insulin Sensitive IS GP07052


title: Suspension arrested fibroblasts (reference) and suspenison-arrested Myoblasts (test) rep2

description:
C2C12 FS48 Vs M S48 Rep 2
Expression profile of differentially expressed genes in suspension arreseted myoblasts

source_name: NIH 3T3_suspenison-arrested Myoblasts (M_S48)

value: NIH3T3 cells suspeneded in semi-solid media


title: KTaj-NSM-SQTP_10-2a


title: Insulin Sensitive IS GP06073


title: Insulin Resistant IR GP06062


title: KTaj-NSM-SHPD_03-1a

value: haloperidol


title: KTaj-NSM-SHPD_1-2a


title: Insulin Sensitive IS GP06056

value: adipose


title: Insulin Resistant IR GP06053


title: Insulin Resistant IR GP06064


title: Insulin Sensitive IS GP06049

value: Insulin Sensitive IS


title: C2C12 myoblasts (reference) vs differentiated myotubes (test) rep2

description:
C2C12 MB Vs MT  Rep 2
Expression profile of differentially expressed genes in suspension arrested myoblasts

hyb_protocol: Purified Cy3,Cy5 Labelled cDNA was incubated on the NIA15K5  chip at 42 degree celsius for 16hrwashed with 1XSSC+02%SDS for 5 min then second wash with 01XSSC+02%SDS for 5 min and third wash with 01XSSC for 5 min and dried the chip by spinning briefly.

scan_protocol: Scanned using  Molecular Dynamics scanner using excitation wavelengths of 543nm and 663nm

data_processing: LOWESS normalized, TIGR MIDAS, background subtracted VALUE data obtained from log2 of processed Experimental signal/processed reference signal

source_name: C2C12_myotubes (MT)

label_protocol: 20 micrograms of RNA is taken for labelling with Cy3/Cy5 dyes Reverse transcription was performed to make cDNA (1hr 30 min at 42 degrees celsius using SuperScript II from Invitrogen) Unincorporated nucleotides were removed using Millipore Spin columns.

tag: culture medium

value: differentiating medium

source_name: C2C12_myoblast (MB)

value: growth medium


title: C2C12 myoblasts (reference) vs differentiated myotubes (test) rep1

description:
C2C12 MB Vs MT  Rep 1
Expression profile of differentially expressed genes in suspension arrested myoblasts

value: differentiation medium


title: Sorted Db-GP33 specific CD8 T cells from infected memory mice, Replicate 3

city: Seattle

first: Surojit

last: Sarkar

state: WA

address: 1100 Olive Way, Suite 100

department: Department of Pediatrics and Laboratory Medicine

institute: University of Washington School of Medicine

description: Pooled total RNA - called the Common Reference Design Pool

hyb_protocol: Hybridizations were performed using Exiqon's protocol. Briefly, the labeled samples were hybridized for 16-18 hours at 60C and then washed sequentially in 3 specially designed buffers at recommended temperatures and conditions.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used. 156 probes that lit up for our mouse samples, the rest of the values were either missing in some samples or the miRNA was not designed for mice.

source_name: Direct ex-vivo splenocytes

label_protocol: Total of 1ug of RNA isolated from FACS sorted CD8 T cells was 3' end labeled with Hy3 following the Exiqon miRCURY LNA Labeling Kit protocol. In parallel, 1ug of Common Reference Design pool RNA was labeled with Cy5 for control. The Common Reference Pool Design control was generated per Exiqon's guidelines by pooling equal amounts of all the experimental RNA samples.

growth_protocol: GP33-41 specific P14 cells were isolated and sorted from mice

extract_protocol: Total RNA extracted using miRNeasy kit (Qiagen) following manufacturer's instructions

tag: days post-infection

value: Day >60 (Memory) following LCMV Armstrong infection

value: Purified CD8 T cells

tag: antigen specificity

value: GP33-41 epitope of LCMV Glycoprotein

source_name: Pooled total RNA from all the experimental samples

value: 4-6 weeks

value: Female


title: Insulin Resistant IR GP06041

value: Insulin Resistant IR


title: Sorted Db-GP33 specific CD8 T cells from infected memory mice, Replicate 1

tag: cell type


title: Sorted Db-GP33 specific CD8 T cells from infected memory mice, Replicate 2


title: KTaj-NSM-SHPD_1-1a

value: Corpus striatum

tag: gender


title: Sorted KLRG-1 Hi / CD127 Lo terminal effector Db-GP33 specific CD8 T cells from infected mice, Replicate 3

value: Day 9 following LCMV Armstrong infection


title: KTaj-NSM-FCQTP_100-2a

source_name: Frontal cortex

value: Frontal cortex

value: quetiapine


title: KTaj-NSM-SC-1a

value: male

value: control

value: vehicle


title: Insulin Sensitive IS GP06001

value: adipose

value: Insulin Sensitive IS


title: Insulin Sensitive IS GP06023


title: KTaj-NSM-FCQTP_100-1a


title: Insulin Sensitive IS GP06042


title: KTaj-NSM-SC-2a


title: Insulin Sensitive IS GP06055


title: KTaj-NSM-FCQTP_10-2a


title: Insulin Sensitive IS GP06002


title: Insulin Resistant IR GP06015


title: Insulin Resistant IR GP04058


title: Insulin Resistant IR GP04103


title: Insulin Resistant IR GP06004


title: Insulin Sensitive IS GP06006


title: KTaj-NSM-SHPD_03-2a

value: haloperidol


title: Sorted KLRG-1 Hi / CD127 Lo terminal effector Db-GP33 specific CD8 T cells from infected mice, Replicate 2


title: Sorted KLRG-1 Lo / CD127 Hi memory precursor Db-GP33 specific CD8 T cells from infected mice, Replicate 2


title: Sorted KLRG-1 Lo / CD127 Hi memory precursor Db-GP33 specific CD8 T cells from infected mice, Replicate 3


title: Sorted KLRG-1 Hi / CD127 Lo terminal effector Db-GP33 specific CD8 T cells from infected mice, Replicate 1


title: Sorted KLRG-1 Lo / CD127 Hi memory precursor Db-GP33 specific CD8 T cells frominfected  mice, Replicate 1


title: Sorted KLRG-1 Hi terminal effector Db-GP33 specific CD8 T cells from infected mice, Replicate 1

value: Day 4.5 following LCMV Armstrong infection


title: Sorted KLRG-1 Hi terminal effector Db-GP33 specific CD8 T cells from infected mice, Replicate 3


title: Sorted KLRG-1 Lo memory precursor Db-GP33 specific CD8 T cells from infected mice, Replicate 3


title: Sorted KLRG-1 Hi terminal effector Db-GP33 specific CD8 T cells from infected mice, Replicate 2


title: KTaj-NSM-FCC-2a


title: Insulin Resistant IR GP02320


title: KTaj-NSM-FCHPD_1-2a


title: Insulin Resistant IR GP03060


title: Insulin Resistant IR GDM010LS


title: KTaj-NSM-FCHPD_03-2a


title: Insulin Resistant IR GP02212


title: KTaj-NSM-FCHPD_1-1a


title: KTaj-NSM-FCHPD_03-1a


title: Sorted Db-GP33 specific CD8 T cells from uninfected mice, Replicate 3

value: Naïve, Uninfected


title: Sorted KLRG-1 Lo memory precursor Db-GP33 specific CD8 T cells from infected mice, Replicate 1

value: Purified CD8 T cells


title: Sorted Db-GP33 specific CD8 T cells from uninfected mice, Replicate 2

value: GP33-41 epitope of LCMV Glycoprotein


title: KTaj-NSM-FCC-1a


title: KTaj-NSM-FCQTP_10-1a


title: Insulin Resistant IR GDM006MT


title: Primary RPCs, biological rep2

city: Shanghai

first: Lu

last: Cui

address: 225 South Chongqing road

institute: Institue of Health Sciences

description: Gene expression data from primary RPCs

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

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

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

source_name: Primary cultured RPCs

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

growth_protocol: For ESCs-RPCs induction, ESCs were suspended in serum free differentiation medium for 3 days to form EBs in the presence of SB431542, an inhibitor of activin receptor-like kinase family (ALK4, 5 and 7), to block Nodal signaling. Then, EBs were plated on Matrigel-coated culture dishes in the RA-free CDM. At day 7 of differentiation, the Sox1+ NPCs (35.8%) were purified by fluorescence-activated cell sorting (FACS). After FACS, the sorted cells were cultured in the N2 medium supplemented with 10 μM DAPT (Calbiochem) and 20 ng/ml bFGF for further induction of retinal progenitor lineages.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ， Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: DKK1 treated ESC-RPCs were performed by addition 1ng/ml recombination DKK1 for 1 days after 1 culture. Primary RPCs were obtained from dissociated nerual retina in postnatal 1 day C57 mice .

value: Retinal progenitor  cells from newborn C57 mice

tag: genetic background

value: untreated


title: Primary RPCs, biological rep3

description: Gene expression data from primary RPCs


title: Normal control ESC-RPCs, biological rep2

description: Gene expression data from normal control ESC-RPCs

source_name: Normal control ESC-RPCs

value: ESC-derived retinal progenitor cells

tag: parental cell line

value: ESC-RPCs were differentiated from 46C ES cell line, which was generated by gene targeting in E14Tg2a.IV ES cells


title: Sorted KLRG-1 Lo memory precursor Db-GP33 specific CD8 T cells from infected mice, Replicate 2

value: 4-6 weeks

value: Female


title: Normal control ESC-RPCs, biological rep3


title: Sorted Db-GP33 specific CD8 T cells from uninfected mice, Replicate 1


title: Primary RPCs, biological rep1

description: Gene expression data from primary RPCs


title: Hela SPAG4 siRNA#2_Hypoxia

city: Tokyo

first: Imari

last: Mimura

address: 4-6-1 Komaba Meguro-ku

department: Laboratory for Systems Biology and Medicine

institute: Research Center for Advanced Science and Technology

description:
Hela Spa2_H
imimura_s06_HelaSpa2H_avg100.txt

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.0. with target intensity=100.

source_name: Hela_SPAG4 KO_hypoxia

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: Hela cells were cultured for 48 hours with knocking down of SPAG4, then cultured for 24 hours under normoxia and 1% hypoxic conditions.

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

treatment_protocol: Two different kinds of sequences for siRNA were used to knockdown of SPAG4 (#1,#2). Hypoxic condition is 1% for 24 hours.

tag: cell line

value: HeLa

tag: genotype/variation

value: SPAG4 knockdown

tag: oxygen level

value: hypoxia


title: Hela Control siRNA_Hypoxia

description:
Hela Co_H
imimura_s04_HelaCoH_avg100.txt

value: control


title: DKK1-treated ESC-RPCs, biological rep3

description: Gene expression data from DKK-treated ESC-RPCs

source_name: DKK1-treated ESC-RPCs

tag: treatment


title: Normal control ESC-RPCs, biological rep1


title: Hela SPAG4 siRNA#1_Normoxia

description:
Hela Spa1_N
imimura_s02_HelaSpa1N_avg100.txt

source_name: Hela_SPAG4 KO_normoxia

value: normoxia


title: Growing C2C12 myoblasts (reference) vs G0 synchronized Myoblasts (test) rep3

description:
C2C12 MB Vs S48 Rep 3
Expression profile of differentially expressed genes in suspension arrested C2C12 cells
G0=S48=quiescence

source_name: C2C12 myoblasts (MB)

value: growth media

source_name: C2C12_G0 synchronized Myoblasts (S48)

value: semi-solid media


title: DKK1-treated ESC-RPCs, biological rep2


title: Growing C2C12 myoblasts (reference) vs G0 synchronized Myoblasts (test) rep1

description:
C2C12 MB Vs S48 Rep 1
Expression profile of differentially expressed genes in suspension arrested C2C12 cells
G0=S48=quiescence


title: Growing C2C12 myoblasts (reference) vs G0 synchronized Myoblasts (test) rep2

description:
C2C12 MB Vs S48 Rep 2
Expression profile of differentially expressed genes in suspension arrested C2C12 cells
G0=S48=quiescence


title: nonTumor_4Month_Urethnae_Nrf2KO

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

description:
Gene expression in non-tumor
NRF2KONT_2_2011

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: The data were analyzed and normalized with GeneSpring software. After normalization, the data was baseline transformed to the median of all samples.

source_name: Non tumor Lung, urethane, replicate 2

label_protocol: 500 ng of total RNA was amplified and labeled using the Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Surface lung tumors were excised, and surrounding tissues were carefully removed under a stereo-microscope. The lung tumors and non-tumor regions of Nrf2+/+- and Nrf2–/–-mice that had been treated with urethane (8 mice/group) were pooled and subjected to a whole-mouse genome microarray analysis. Total RNA was extracted from the tissues using ISOGEN (Nippon Gene). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mouse lung tumors were induced after 4 month later by the intraperitoneal injection of urethane (1-g/kg body weight).

tag: genotype

value: ICR

value: lung

value: female

tag: age

value: 6 months


title: LungTumor_4Month_Urethnae_wt

description:
Gene expression in tumor
NRF2WTLT_3_2011

source_name: Lung tumor, urethane, replicate 3

value: lung tumor


title: LungTumor_4Month_Urethnae_Nrf2KO

description:
Gene expression in tumor
NRF2KOLT_4_2011

source_name: Lung tumor, urethane, replicate 4


title: mouse ES cells 2

status: Public on Apr 15 2013

city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

institute: Max Planck Institute of Psychiatry

description:
ESC_2
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw probe level intensity values were normalized using a variance stabilization approach by employing the R function vsn2 from the corresponding vsn package (Huber et al., 2002).

source_name: mESC

label_protocol: 500ng of total RNA was amplified and labeled using the Illumina Total Prep RNA Amplification Kit (Ambion, AMIL1791) according to the manufacturers’ instructions

growth_protocol: Mouse Pluripotent Stem Cell Culture:   All mouse PSC lines; AV3, p2lac40, Sox17GFP, Pax9Venus, were maintained on mouse embryonic fibroblasts in KO DMEM (GIBCO, 10829) supplemented with 15% Hyclone FBS (Thermo Scientific, SH30070.03), 1% Glutamax (GIBCO, 35050079), 1% NEAA (Cellgro, 25-025-CI), 100µM β-mercaptoethanol (Invitrogen, 21985023), 1x103 units/ml ESGRO LIF (Millipore, ESG1107). Cells were fed daily and split every 2-3 days with 0.25% trypsin (GIBCO, 25200114).

extract_protocol: RNA was isolated using Trizol (Invitrogen, 15596-018) according to the manufacturer’s instructions.

treatment_protocol: Mouse PSC Differentiation:   Maintenance cultures were split and MEF depleted for 30 minutes in maintenance media. PSCs were collected and resuspended in differentiation media 1 [A-DMEM (GIBCO, 12491) supplemented with 1% N2 (GIBCO, 17502-048), 2% B27 minus vitamin A (GIBCO, 12587-010), 1% Glutamax (GIBCO, 35050079) 1% P/S (Cellgro, 30-001-CI)] and 10µM Y-27632 (Selleck Chemicals, S1049). Cells were plated at 5x103 cells/cm2 onto 0.1% gelatin-coated 6 well plates. On day 2 cells were fed with differentiation media 1 with 5nM GSKiXV (Calbiochem, 361558) and 5µM IDE-1 (Tocris, 4015). On days 3, 4, and 5, cells were fed with differentiation media 2 [A-DMEM (GIBCO, 12491) supplemented with 2% B27 minus vitamin A, 1% Glutamax, 1% P/S] plus 5µM IDE-1. On day 6 cultures were split with 0.25% trypsin and plated at 3x105 cells/cm2 onto 804G conditioned medium-coated plates with 10µM Y-27632 in differentiation media 2. Cells were treated with 500nM A83-01 (Tocris, 2939) and 100nM LDN193189 (Selleck Chemicals, S2618).

value: ES cells

value: E


title: DKK1-treated ESC-RPCs, biological rep1

value: ESC-derived retinal progenitor cells

value: ESC-RPCs were differentiated from 46C ES cell line, which was generated by gene targeting in E14Tg2a.IV ES cells


title: nonTumor_4Month_Urethnae_wt

description:
Gene expression in non-tumor
NRF2WTNT_1_2011

source_name: Non tumor lung, urethane, replicate 1


title: Hela SPAG4 siRNA#1_Hypoxia

description:
Hela Spa1_H
imimura_s05_HelaSpa1H_avg100.txt


title: Hela SPAG4 siRNA#2_Normoxia

description:
Hela Spa2_N
imimura_s03_HelaSpa2N_avg100.txt


title: Hela Control siRNA_Normoxia

description:
Hela Co_N
imimura_s01_HelaCoN_avg100.txt


title: mouse ES cells 1

description:
ESC_1
replicate 1

value: D


title: in vitro derived definitive endoderm 3

description:
DE_Endoderm_3
replicate 3

value: 129X1/SvJ x 129S1/SV-+p+Tyr- cKitlSl-J/+

value: in vitro derived definitive endoderm

value: C


title: mouse ES cells 3

description:
ESC_3
replicate 3


title: in vitro derived anterior foregut 2

description:
AFE_2
replicate 2

value: in vitro derived anterior foregut

value: G


title: in vitro derived anterior foregut 3

description:
AFE_3
replicate 3

value: H


title: in vitro derived anterior foregut 1

description:
AFE_1
replicate 1

value: F


title: in vitro derived definitive endoderm 2

description:
DE_Endoderm_2
replicate 2

value: B


title: in vitro derived definitive endoderm 1

description:
DE_Endoderm_1
replicate 1

value: A


title: Replication timing of MEL cell line, replicate 2

description: Submitted as of 3-28-13

source_name: Early-replicating DNA of MEL cell line

value: Unknown

value: M

source_name: Late-replicating DNA of MEL cell line


title: Replication timing of CH12 cell line, replicate 2

description: Submitted as of 3-28-13

source_name: Early-replicating DNA of CH12 cell line

source_name: Late-replicating DNA of CH12 cell line


title: Replication timing of CH12 cell line, replicate 1

description: Submitted as of 3-28-13


title: Replication timing of MEL cell line, replicate 1

description: Submitted as of 3-28-13


title: osteosarcoma 29 (SNP)

city: Amsterdam

first: Joeri

last: Both

state: Noord Holland

address: Meibergdreef 9

department: Genome Analysis

institute: Amsterdam Medical Center

description: Genomic DNA extracted from osteosarcomas was genotyped using HumanCNV370-Quad BeadChips (Illumina).

hyb_protocol: Standard hyb protocol (Illumina)

scan_protocol: Standard scan protocol (Illumina)

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

source_name: osteosarcoma

label_protocol: Standard label protocol (Illumina), 200 ng of genomic DNA as start material

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using proteinase K and high salt precipitation, washed with EtOH, air dried, resuspended in TE.

value: Female

tag: type of material

value: biopsy

tag: location

value: ilium

value: osteosarcoma tumor


title: osteosarcoma 16 (SNP)

value: Male

value: humerus

tag: tissue


title: osteosarcoma 27 (SNP)

value: femur


title: osteosarcoma 20 (SNP)


title: osteosarcoma 9 (SNP)

value: metastasis

value: lung

value: metastatic lung osteosarcoma tumor


title: osteosarcoma 17 (SNP)

value: resection


title: osteosarcoma 14 (SNP)


title: osteosarcoma 19 (SNP)


title: osteosarcoma 5 (SNP)


title: osteosarcoma 32 (SNP)


title: osteosarcoma 12 (SNP)

value: tibia


title: osteosarcoma 25 (SNP)


title: osteosarcoma 23 (SNP)


title: osteosarcoma 28 (SNP)


title: osteosarcoma 18 (SNP)


title: osteosarcoma 22 (SNP)


title: osteosarcoma 24 (SNP)


title: osteosarcoma 13 (SNP)


title: osteosarcoma 10 (SNP)


title: osteosarcoma 11 (SNP)


title: osteosarcoma 7 (SNP)


title: SCC24

city: Seville

first: Sonia

last: Molina-Pinelo

address: Avda. MAnuel Siurot s/n

institute: IBIS

description: test

data_processing: Relative quantification of gene expression was determined using the comparative cycle threshold method (2(-ddCt)) as previously described Ref : Livak, K. J., and T. D. Schmittgen. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402-408. .

label: FAM

source_name: Tumoral tissue

label_protocol: FAM

extract_protocol: Total RNA, containing small RNA, was extracted from tumour tissue sample by mirVana miRNA isolation kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions.

value: NSCLC

tag: histologic subtype in nsclc

value: Squamous cell lung cancer


title: SCC23

description: test


title: osteosarcoma 31 (SNP)


title: osteosarcoma 30 (SNP)


title: SCC22

description: test


title: SCC18

description: test


title: SCC15

description: test


title: SCC19

description: test


title: SCC14

description: test


title: SCC21

description: test


title: SCC20

description: test


title: SCC17

description: test


title: SCC12

description: test


title: SCC11

description: test


title: osteosarcoma 15 (SNP)


title: SCC8

description: test


title: osteosarcoma 26 (SNP)


title: osteosarcoma 21 (SNP)


title: SCC10

description: test


title: SCC6

description: test


title: SCC7

description: test


title: SCC5

description: test


title: SCC16

description: test


title: SCC13

description: test


title: SCC4

description: test


title: SCC9

description: test


title: SCC3

description: test


title: SCC2

description: test


title: SCC1

description: test