title: jejunum_control_rep3

description: Gene expression of 6 weeks rat's jejunum

source_name: Jejunum, control, replicate 3

value: Sprague-Dawley

value: jejunum

value: control


title: CAOV3

status: Public on Sep 18 2014

type: RNA

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

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

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Ovarian cancer cell-line

label_protocol: Standard Affymetrix protocol

growth_protocol: Cell lines were grown according to standard conditions (RPMI-1640 glutamax-Gibco/Invitrogen- supplemented with 10% FCS, 100 U/ml penicillin, 100 µg/ml streptomycin, 50 µg/ml gentamycin).

extract_protocol: Cells were directly lysed in the culture flasks and total RNA was extracted with RNABee (Campro, Veenendaal, the Netherlands) according to the manufacturer procedure

tag: cell line

tag: morphology

value: Epithelial


title: A2780

value: Round


title: Genome-wide occupancy of Med7p in yeast conditions (replica 1)

type: genomic

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

country: Canada

institute: CHU Québec

description:
Med7p-yeast(R1)
Starting from sequences from the C. albicans Genome Assembly 21, we extracted a continuous series of 242,860 60-bp oligonucleotides each overlapping by 1 bp. We then eliminated 2062 probes containing stretches of 13 or more A or T nucleotides. The remaining 240,798 sequences were then used to produce an antisense (Crick) whole genome tiling array using the Agilent Technologies eArray service (https://earray.chem.agilent.com/earray/).

hyb_protocol: The microarray slides were pre-hybridized for 1 hour at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. The slides were washed twice for 10 min at 42°C with 1x SSC, 0.1% SDS, twice for 10 min at 37°C with 0.1x SSC, 0.1% SDS, and finally, with quick consecutive washes in three 0.1x SSC baths. Slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: ChIP-Chip data was normalized as described by Lavoie et al. (2010) PLoS Biol 8(3): e1000329.

molecule: genomic DNA

organism: Candida albicans

source_name: WT under yeast conditions (YPD 30oC) - Input sample

label_protocol: Indirect labeling with Cy3 and Cy5 was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. The labeled DNA was purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: ChIP-chip experiment was performed as described by Lavoie et al. BMC Genomics 2008, 9:578. RNAs were extracted as described by Sellam et al. (2009) Eukaryotic Cell 8 (8), 1174-1183, using the RNeasy Mini kit (Qiagen).

treatment_protocol: For ChIP-chip analysis, an overnight cultures in YPD were diluted to OD600nm =0.2 and grown to OD600nm=2 in 40 ml YPD at 30oC.

tag: strain/background

tag: genotype/variation

value: WT

tag: cell type

value: yeast-form cells

tag: chip antibody

value: IgG-Sepharose 6 beads Fast Flow (GE Healthcare, catalog number 17-0969-01)

source_name: Med7p-TAP under yeast conditions (YPD 30oC) - ChIP sample


title: seedling,1.5h_after_Gamma,WT rep2

city: Davis

first: Anne

last: Britt

state: CA

address: One Shields Drive

department: Plant Biology

country: USA

institute: UC Davis

hyb_protocol: Subsequently, 10 μg of this fragmented target cRNA was hybridized at 45°C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix ATH1 array. The GeneChip arrays were washed and then stained with SAPE (streptavidin–phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was performed on a GeneChip Scanner 3000.

data_processing: The results were quantified and analyzed using GCOS 1.2 software (Affymetrix Inc.) with default values (scaling, target signal intensity = 500; normalization, all probe sets; parameters, all set at default values).  The data was normalized using RMA from the R package affy.  To generate the matrix of expression values here, normalization was performed simultaneously across all samples.  NOTE: When generating the results reported in the paper itself, normalization was performed separately for each experimental condition/control condition pair, normalizing only across the 4 samples associated with that specific experimental or control condition.

organism: Arabidopsis thaliana

source_name: seedling_1.5h after Gamma irradiation_WT

label_protocol: Single-stranded and then double-stranded cDNA was synthesized from the poly(A)+ mRNA present in the isolated total RNA (typically 10 μg total RNA starting material for each sample reaction) using the SuperScript double-stranded cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA) and poly(T) nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting double-stranded cDNA was used as a template to generate biotin-tagged cRNA from the Affymetrix GeneChip IVT labeling kit, and 15 μg of the resulting biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35–200 bases) following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

growth_protocol: Five days prior to irradiation, the plates were placed vertically in a 21°C growth chamber in the BNL Controlled Environment Facility, where plants grew under cool white lamps (16 h day) until the time of irradiation.

extract_protocol: Approximately 30-40 plants were harvested and pooled together for total RNA extraction (RNeasy Mini-Prep; Qiagen, Valencia, CA, USA). Eluted total RNAs were quantified with a portion of the recovered total RNA adjusted to a final concentration of 1.25 μg μl-1.

treatment_protocol: For irradiation, plates were moved either to the Controlled Environment Radiation Facility for exposure to gamma radiation (100 Gy at 7 Gy/min), or to the National Space Radiation Laboratory (NSRL) for exposure to accelerated 1 GeV/n 56Fe particles (30 Gy at 2.5 Gy/min).

value: wild type

tag: age

value: 5 days old

tag: treated with

value: 100 Gy of Gamma radiation

tag: treatment duration

value: 15 minutes

tag: sampling time

value: 10:10 am on Day #1

tag: time after treatment


title: 59M

value: Spindle


title: Liver_LowGlucoseHS32_genotype

city: Milwaukee

first: Leah

middle: C

last: Solberg Woods

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Genome-wide 10K SNP array in heterogeneous stock rats

hyb_protocol: The Affymetrix 10K SNP array was selected for these studies for its overall comprehensive coverage.  Samples are hybridized overnight.

scan_protocol: After hybridization, arrays were washed and sarrays are washed and loaded onto the Affymetrix GeneChip Scanner 3000

data_processing: All SNPs were given a call rate.  Those that did not reach a sufficient call rate were removed.

organism: Rattus norvegicus

source_name: heterogeneous stock rat tail

label_protocol: Targeted genotyping technology was used.  Two PCR reactions occur: the first is to amplify the targeted region and the second is to label the region for subsequent detection.

growth_protocol: Male rats were maintained two per cage and fed ad libitum.  Rats were euthanized at 17 weeks of age after an overnight fast.

extract_protocol: Genomic DNA was extracted using the Qiagen DNeasy kit

treatment_protocol: Rats were fasted overnight prior to being euthanized.

tag: strain

value: heterogeneous stock

tag: phenotype

value: Low Glucose

tag: tissue

value: tail

tag: gender

value: male


title: A2780 (ECACC)


title: jejunum_control_rep2

city: Beijing

first: peng

last: yin

state: Other

address: China Agricultural University (CAU), Beijing 100193, PR China

country: China

institute: CAU-BUA TCVM Teaching and Researching Team, College of Veterinary Medicine, China Agricultural University

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)

source_name: Jejunum, control, replicate 2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

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 mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Sprague-Dawley rats weighing 200 ± 20 g were housed at 25°C and 60% relative humidity for 1 week. On the eighth day, the rats were randomly divided into control and 3day stress (S3d) groups. Ten rats in each group were housed in plastic cages (400 mm × 300 mm × 180 mm) with a layer of softwood chips and provided free access to food and water. Rats from each group were anesthetized by ether inhalational anesthesia, exsanguinated immediately after anesthesia, and then sacrificed. Sections of the jejunum were rapidly excised，a 3-cm section were washed using physiological saline (0.9%), then minced and separated into four sample tubes, frozen in liquid nitrogen, and stored at −80°C

value: Sprague-Dawley

value: jejunum

tag: age (weight)

tag: treatment


title: jejunum_control_rep1

source_name: Jejunum, control, replicate 1

value: control


title: PC12_MAXVector_rep2

city: Madrid

first: Mercedes

last: Robledo

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: Gene Expression after transfection and selection with E418.

hyb_protocol: Hybridizations with 1.65 μg of Cy3- cRNA were performed according to the respective manufacturer’s instructions.

scan_protocol: Microarrays were scanned with a G2505C DNA microarray scanner (Agilent).

data_processing: Images were analyzed by Agilent Feature Extraction Software (v.10.7), which performed feature quantitation and additive detrend correction. No background subtraction was performed. Gene expression profiles were normalized using GeneSpring Studio (Agilent).

source_name: Rat pheochromocytoma cells (PC12)

label_protocol: 100 ng of total RNA was used for fluorescently labeled cRNA synthesis with the One Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit according to manufacturer’s recommendations (Agilent, Santa Clara, CA).

growth_protocol: PC12 cells (ATCC) were cultured in F-12K medium (ATCC) with 2.5% fetal calf serum and 15% horse serum in Corning CellBIND flasks.

extract_protocol: Total RNA was isolated using TRIreagent (MRC, Cincinnati, OH,USA) and purified using the Rneasy Mini Kit (Qiagen). DNAse treatment was performed using the DNA-free Kit (Ambion).

treatment_protocol: PC12 cells were transfected using the 4D-Nucleofector (Lonza, Allendale, USA).Optimal conditions were established using the pmaxGFP vector and the cell line optimization 4D-Nucleofector X kit (Lonza). The SF cell line Nucleofector kit (Lonza) in combination with transfection program CM-167 for PC12 achieved the highest transfection efficiency and least toxicity. Nucleofection was performed as described previously (Zeitelhofer et al., 2007). In brief, 1.6 to 8.0x106 cells and 5 μg of plasmid DNA, were added to 100 μl of the Nucleofetor solution.

tag: cell line

value: pheochromocytoma


title: PC12_MAXVector_rep1


title: PC12_EmptyVector_rep1


title: PC12_EmptyVector_rep2


title: tissue_normal_480_rep3

city: Chongqing

first: Kai

last: Wang

address: Sha pingba

institute: Third Military Medical University

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

scan_protocol: Axon GenePix 4000B microarray scanner and GenePix pro V6.0 software

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).
Condition pairs: test_vs_control, Fold Change cut-off: 2.0, P-value cut-off: 0.05

source_name: adjacent normal esophageal tissue

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

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

value: Male

tag: tumor stage

value: Normal


title: tissue_normal_478_rep4


title: tissue_normal_471_rep1


title: tissue_cancer_478_rep4

source_name: esophageal tumor


title: Liver_HighGlucoseHS31_genotype

value: High Glucose


title: Liver_LowGlucoseHS30_genotype


title: tissue_cancer_471_rep1


title: Liver_LowGlucoseHS26_genotype


title: Liver_HighGlucoseHS28_genotype


title: tissue_normal_482_rep2


title: Liver_LowGlucoseHS27_genotype


title: 2774

tag: morphology

value: Epithelial


title: Liver_HighGlucoseHS24_genotype


title: Liver_LowGlucoseHS25_genotype


title: tissue_cancer_480_rep3


title: Liver_LowGlucoseHS29_genotype


title: PCC-primary_tumor-rep1 (NF1_8)

hyb_protocol: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 825 ng. Volume: 100 uL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent).

data_processing: Images were analyzed by Agilent Feature Extraction Software (ver. 10.7), which performed feature quantitation and additive detrend correction. No background subtraction was performed.

source_name: PCC, primary tumor

label_protocol: 500 ng of total RNA were amplified by double strand cDNA synthesis, followed by T7-based in vitro transcription, according to the manufacturer’s instructions. 100ng of amplified cRNA was then labeled with cyanine (Cy)5-conjugated 2′-deoxyuridine 5′-triphosphate, whereas cRNA from Universal Human Reference RNA was labeled with Cy3-conjugated 2′-deoxyuridine 5′-triphosphate using the commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 of May 2010.

tag: tumor tissue

value: PCC, primary tumor

tag: mutation

source_name: Universal Human Reference RNA (Stratagene)

tag: reference

value: Universal Human Reference RNA (commercial RNA from Stratagene)


title: PCC-primary_tumor-rep1 (NF1_6)


title: tissue_cancer_482_rep2

tag: age


title: PCC-primary_tumor-rep1 (SP_16)

value: Sporadic


title: Male WSR-2 Air Pool 1 8hr

status: Public on Sep 17 2014

city: Portland

first: Marina

last: Guizzetti

state: OR

address: 3710 SW US Veterans Hospital Rd

department: Behavioral Neuroscience

institute: Oregon Health & Science University; Portland VA Research Service

hyb_protocol: Hybridization with complex labeled RNA probe was performed overnight at 50 degrees C with 20 ml Ultra-Array hybridization buffer (Ambion).  The final post hybridization wash was at 50 degrees C in 0.5 x SSC, 0.5% SDS.

scan_protocol: Microarrays were exposed to storage phosphor screens for 2 h and scanned at high resolution with a Cyclone phosphorimager and OptiQuant software (Perkin Elmer).

data_processing: Raw intensity values, determined with Pathways v4 Software (Research Genetics), were log2-transformed, converted to z-scores, multiplied by 2 and added to eight so that each array has a mean of 8, a variance of 4, and a standard deviation of 2.

organism: Mus musculus

source_name: prefrontal cortex

label_protocol: Rnase treated total RNA isolated from the PFC of two animals (2.5 micrograms each) was pooled for each complex probe labeling reaction.  Probe labeling from the total RNA mixture was performed by linear synthesis with 33P-dATP incorporation using the Array Advantage kit (Ambion) using anchored oligo-dT primers and M-MLV reverse transcriptase with a 42 degree C incubation for 2 hours.  Complex probes were purified by passage through a NucAway spin column.

extract_protocol: Total RNA was extracted from the PFC using RNA  STAT-60 (Tel-Test, Inc.) according to the manufacturers protocol.  Contaminating genomic DNA was  removed by digestion with Rnase free Dnase followed by Zymo-spin column purification according to the manufacturer's recommendations (Zymo Research).

treatment_protocol: Two independently derived replicate Withdawal-Seizure Prone (WSP) and Withdrawal-Seizure Resistant (WSR) were derived by selective breeding for divergent withdrawal severity from genetically heterogeneous HS/Ibg mice.  Female and male mice from both replicates were tested for expression differences.  To identify phenotype-specific differences, expression analysis was collapsed on replicate for each selected line.  Mice were maintained under a light/dark cycle of 0600-1800 light with water and Purina Lab Diet Chow available ad libitum.  Room temperatures were maintained at 22 +/- 1 degree celcius.  All animal procedures were approved by the Portland Oregon VA Medical Center Institutional Animal Care and Use committee and followed US National Institutes of Health animal welfare guidelines.  Mice were made dependent upon Ethanol (EtOH) using a method of vapor inhalation in chambers manufactured in-house, with modifications previously published (Beadles-Bohline and Wiren, 2006).  Drug-naive adult mice from selected generation 26 (filial generation G87-G116) were used.  EtOH exposure was initiated at 0800 h.  On day one EtOH mice were weighed, injected i.p. with EtOH at 1.5 g/kg for WSP-1, WSR-1, WSR-2 and1.75 g/kg for WSP-2 animals, necessary to maintain similar blood EtOH concentrations between the selected lines, and 68.1 mg/kg pyrazole HCl.  Control animal were placed into air chambers and received pyrazole only.  All mice again received pyrazole (68.1 mg/kg) at 24 h and 48 h to reduce fluctuations in BEC.  EtOH exposed mice had 20 microliters of blood take from the tail for daily BEC determination.  Following 72 h of constant EtOH vapor exposure, all mice were removed from the chambers, weighed, and had tail blood samples drawn for BEC determination by gas chromatography as previously described.  Prefronal cortex (PFC) was isolated by dissection from whole brain by first discarding the olfactory bulb and making a coronal slice 2 mm into the frontal region of the cortex.  Lateral regions were removed by cutting the tissue at a 45 degree angle with the lobes facing upward.

tag: Sex

tag: selected line

value: WSR

tag: selected line rep

value: Control

tag: biological replicate

tag: time point

value: 8hr withdrawal


title: Male WSR-1 EtOH Pool 1 8hr

value: Ethanol vapor


title: Male WSR-2 EtOH Pool 2 8hr


title: Male WSR-2 Air Pool 2 8hr


title: Male WSR-1 EtOH Pool 2 8hr


title: PCC-primary_tumor-rep1 (MAX_5)

value: MAX


title: Male WSR-2 EtOH Pool 1 8hr


title: PCC-primary_tumor-rep1 (MAX_7)


title: PCC-primary_tumor-rep1 (NF1_3)


title: PCC-primary_tumor-rep1 (NF1_1)


title: ES2

value: Spindle


title: PCC-primary_tumor-rep1 (MAX_4)


title: Male WSP-1 Air Pool 1 8hr

value: WSP


title: Male WSP-2 EtOH Pool 2 8hr


title: Male WSP-2 EtOH Pool 1 8hr


title: Male WSR-1 Air Pool 1 8hr


title: Male WSP-1 Air Pool 2 8hr


title: Male WSP-2 Air Pool 1 8hr


title: Male WSP-1 EtOH Pool 1 8hr


title: Female WSR-2 EtOH Pool 1 8hr

value: Female


title: Male WSP-2 Air Pool 2 8hr


title: Male WSR-1 Air Pool 2 8hr


title: Male WSP-1 EtOH Pool 2 8hr


title: Female WSR-1 EtOH Pool 2 8hr


title: Female WSR-2 EtOH Pool 2 8hr


title: Female WSR-1 EtOH Pool 1 8hr


title: PCC-primary_tumor-rep1 (MAX_1)


title: Female WSR-1 Air Pool 2 8hr


title: Female WSP-2 EtOH Pool 2 8hr


title: Female WSP-2 Air Pool 2 8hr


title: Female WSR-1 Air Pool 1 8hr


title: Female WSP-2 Air Pool 1 8hr


title: Female WSR-2 Air Pool 1 8hr


title: Female WSP-1 EtOH Pool 1 8hr


title: Female WSP-1 EtOH Pool 2 8hr


title: Male WSR-2 Air Pool 2 0hr

value: 0hr withdrawal


title: Female WSP-2 EtOH Pool 1 8hr


title: Female WSP-1 Air Pool 2 8hr


title: Female WSP-1 Air Pool 1 8hr


title: Male WSR-2 EtOH Pool 2 0hr


title: Male WSP-2 EtOH Pool 1 0hr


title: Male WSP-2 Air Pool 1 0hr


title: Male WSP-2 Air Pool 2 0hr


title: Female WSR-2 EtOH Pool 1 0hr

description: Excluded from analysis


title: Male WSP-2 EtOH Pool 2 0hr


title: Male WSR-1 Air Pool 2 0hr


title: Male WSP-1 EtOH Pool 2 0hr


title: Female WSR-2 EtOH Pool 2 0hr


title: Male WSR-1 EtOH Pool 2 0hr


title: Male WSR-2 Air Pool 1 0hr


title: Male WSR-1 Air Pool 1 0hr


title: Male WSP-1 Air Pool 2 0hr


title: Male WSP-1 EtOH Pool 1 0hr


title: Male WSP-1 Air Pool 1 0hr


title: Female WSR-2 Air Pool 2 0hr


title: Male WSR-1 EtOH Pool 1 0hr


title: Male WSR-2 EtOH Pool 1 0hr


title: Female WSR-2 Air Pool 2 8hr


title: Female WSR-1 EtOH Pool 2 0hr


title: Female WSR-2 Air Pool 1 0hr


title: Female WSR-1 Air Pool 2 0hr


title: Female WSR-1 EtOH Pool 1 0hr


title: Female WSR-1 Air Pool 1 0hr


title: Female WSP-2 EtOH Pool 1 0hr


title: Female WSP-1 EtOH Pool 1 0hr


title: Female WSP-1 Air Pool 1 0hr


title: Female WSP-2 Air Pool 2 0hr


title: Female WSP-2 Air Pool 1 0hr


title: Female WSP-1 Air Pool 2 0hr


title: Female WSP-2 EtOH Pool 2 0hr


title: Female WSP-1 EtOH Pool 2 0hr


title: VAT_98

city: Groningen

first: Lude

last: Franke

state: Please Select

address: Hanzeplein 1

department: Genetics

institute: UMCG

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting

data_processing: SWAN Normalization and M-value transformation, using minfi (v.1.8.9) and R (v.3.0.2)

label: Cy5 and Cy3

source_name: severely obese patient_visceral adipose tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from liver samples using the AllPrep DNA/RNA/Protein Mini kit (QIAgen, Hilden, Germany) according to standard instructions

tag: subject status

value: severely obese patient

value: male

tag: subject age

tag: bmi

value: visceral adipose tissue


title: VAT_111

tag: gender

value: female

tag: tissue


title: VAT_121


title: VAT_90


title: VAT_105


title: VAT_100


title: VAT_58


title: VAT_103


title: VAT_86


title: VAT_115


title: VAT_87


title: VAT_77


title: VAT_61


title: VAT_92


title: VAT_60


title: VAT_110


title: VAT_99


title: VAT_68


title: VAT_97


title: VAT_78


title: VAT_93


title: VAT_76


title: VAT_84


title: VAT_113


title: VAT_56


title: VAT_117


title: VAT_74


title: VAT_62


title: VAT_130


title: VAT_112


title: VAT_75


title: VAT_40


title: VAT_104


title: VAT_124


title: VAT_128


title: VAT_122


title: VAT_70


title: VAT_95


title: VAT_53


title: VAT_79


title: VAT_120


title: VAT_73


title: VAT_63


title: VAT_36


title: VAT_89


title: VAT_96


title: VAT_102


title: VAT_59


title: VAT_69


title: VAT_123


title: VAT_52


title: VAT_42


title: VAT_131


title: VAT_106


title: VAT_116


title: VAT_85


title: VAT_66


title: VAT_83


title: VAT_107


title: VAT_54


title: VAT_51


title: VAT_114


title: VAT_71


title: VAT_88


title: VAT_45


title: VAT_127


title: VAT_125


title: VAT_37


title: Muscle_79

source_name: severely obese patient_muscle

value: muscle


title: VAT_64


title: Muscle_77


title: VAT_55


title: VAT_48


title: Muscle_99


title: Muscle_102


title: Muscle_73


title: Muscle_110


title: Muscle_111


title: Muscle_98


title: Muscle_59


title: Muscle_66


title: Muscle_105


title: Muscle_97


title: Muscle_93


title: Muscle_130


title: Muscle_121


title: Muscle_116


title: Muscle_74


title: Muscle_113


title: Muscle_71


title: Muscle_56


title: Muscle_63


title: Muscle_40


title: Muscle_124


title: Muscle_103


title: Muscle_127


title: Muscle_125


title: Muscle_64


title: Muscle_114


title: Muscle_89


title: Muscle_84


title: Muscle_123


title: Muscle_90


title: Muscle_109


title: Muscle_68


title: Muscle_131


title: Muscle_107


title: Muscle_128


title: Muscle_120


title: Muscle_117


title: Muscle_112


title: Muscle_87


title: Muscle_36


title: Muscle_69


title: Muscle_55


title: Muscle_51


title: Muscle_37


title: Muscle_78


title: Muscle_60


title: Muscle_45


title: Muscle_42


title: Muscle_85


title: Muscle_43


title: Muscle_119


title: Muscle_88


title: Muscle_54


title: Muscle_91


title: Muscle_92


title: Muscle_83


title: SAT_105

description:
SAT sample of Morbidly patient
5822943029_R05C01

source_name: severely obese patient_Subqutaneous adipose tissue

value: Subqutaneous adipose tissue


title: Muscle_106


title: SAT_90

description:
SAT sample of Morbidly patient
5822943029_R05C02


title: Muscle_41


title: SAT_83

description:
SAT sample of Morbidly patient
5822943019_R06C01


title: SAT_53

description:
SAT sample of Morbidly patient
5822791030_R06C02


title: SAT_92

description:
SAT sample of Morbidly patient
5822943026_R01C02


title: SAT_112

description:
SAT sample of Morbidly patient
5822943026_R04C01


title: SAT_120

description:
SAT sample of Morbidly patient
5822943019_R04C02


title: SAT_89

description:
SAT sample of Morbidly patient
5822943015_R02C01


title: SAT_56

description:
SAT sample of Morbidly patient
5822943029_R01C02


title: SAT_116

description:
SAT sample of Morbidly patient
5822943014_R04C01


title: SAT_74

description:
SAT sample of Morbidly patient
5822943028_R02C01


title: SAT_51

description:
SAT sample of Morbidly patient
5822943015_R06C01


title: SAT_76

description:
SAT sample of Morbidly patient
5822943026_R04C02


title: SAT_86

description:
SAT sample of Morbidly patient
5822943014_R02C02


title: SAT_109

description:
SAT sample of Morbidly patient
5822943015_R02C02


title: SAT_121

description:
SAT sample of Morbidly patient
5822943014_R01C02


title: SAT_60

description:
SAT sample of Morbidly patient
5822943013_R02C01


title: SAT_119

description:
SAT sample of Morbidly patient
5822943028_R04C01


title: SAT_124

description:
SAT sample of Morbidly patient
5822791029_R02C02


title: SAT_78

description:
SAT sample of Morbidly patient
5822791030_R03C01


title: SAT_113

description:
SAT sample of Morbidly patient
5822791029_R06C02


title: SAT_42

description:
SAT sample of Morbidly patient
5822943028_R06C01


title: SAT_71

description:
SAT sample of Morbidly patient
5822791029_R02C01


title: SAT_100

description:
SAT sample of Morbidly patient
5822791028_R05C01


title: SAT_68

description:
SAT sample of Morbidly patient
5822791027_R01C02


title: SAT_125

description:
SAT sample of Morbidly patient
5822791027_R03C02


title: SAT_127

description:
SAT sample of Morbidly patient
5822791030_R04C01


title: SAT_52

description:
SAT sample of Morbidly patient
5822791030_R01C01


title: SAT_55

description:
SAT sample of Morbidly patient
5822791026_R06C02


title: SAT_79

description:
SAT sample of Morbidly patient
5822791028_R04C02


title: SAT_43

description:
SAT sample of Morbidly patient
5822943013_R03C01


title: SAT_123

description:
SAT sample of Morbidly patient
5822791026_R02C02


title: SAT_131

description:
SAT sample of Morbidly patient
5822791026_R06C01


title: SAT_85

description:
SAT sample of Morbidly patient
5822791024_R05C02


title: SAT_91

description:
SAT sample of Morbidly patient
5822791024_R02C01


title: SAT_117

description:
SAT sample of Morbidly patient
5822791027_R04C02


title: SAT_96

description:
SAT sample of Morbidly patient
5822791026_R01C01


title: SAT_45

description:
SAT sample of Morbidly patient
5822791024_R06C01


title: SAT_66

description:
SAT sample of Morbidly patient
5822791024_R04C02


title: SAT_122

description:
SAT sample of Morbidly patient
5822791024_R02C02


title: SAT_103

description:
SAT sample of Morbidly patient
5822791019_R06C02


title: SAT_104

description:
SAT sample of Morbidly patient
5822791026_R05C02


title: SAT_111

description:
SAT sample of Morbidly patient
5822791024_R06C02


title: SAT_84

description:
SAT sample of Morbidly patient
5822791018_R04C01


title: SAT_114

description:
SAT sample of Morbidly patient
5822791015_R01C02


title: SAT_99

description:
SAT sample of Morbidly patient
5822791018_R05C01


title: SAT_88

description:
SAT sample of Morbidly patient
5822791018_R06C01


title: SAT_64

description:
SAT sample of Morbidly patient
5822791024_R03C01


title: SAT_40

description:
SAT sample of Morbidly patient
5822791018_R02C02


title: SAT_115

description:
SAT sample of Morbidly patient
5822791015_R06C01


title: SAT_97

description:
SAT sample of Morbidly patient
5822791013_R01C02


title: SAT_62

description:
SAT sample of Morbidly patient
5822791019_R05C02


title: SAT_41

description:
SAT sample of Morbidly patient
5822791018_R01C02


title: SAT_106

description:
SAT sample of Morbidly patient
5822791012_R05C02


title: SAT_95

description:
SAT sample of Morbidly patient
5822791018_R03C02


title: SAT_37

description:
SAT sample of Morbidly patient
5822791002_R05C01


title: SAT_63

description:
SAT sample of Morbidly patient
5822791012_R02C01


title: SAT_77

description:
SAT sample of Morbidly patient
5822791011_R03C02


title: SAT_93

description:
SAT sample of Morbidly patient
5822791012_R03C01


title: SAT_98

description:
SAT sample of Morbidly patient
5822791008_R04C01


title: SAT_73

description:
SAT sample of Morbidly patient
5822791002_R01C01


title: SAT_107

description:
SAT sample of Morbidly patient
5822791002_R04C02


title: SAT_48

description:
SAT sample of Morbidly patient
5822791001_R03C02


title: SAT_110

description:
SAT sample of Morbidly patient
5822791015_R04C02


title: SAT_70

description:
SAT sample of Morbidly patient
5822791003_R04C02


title: Liver_105

description:
Liver sample of Morbidly patient
5822943028_R01C01

source_name: severely obese patient_liver

value: liver


title: SAT_75

description:
SAT sample of Morbidly patient
5822791003_R02C02


title: Liver_109

description:
Liver sample of Morbidly patient
5822943029_R01C01


title: SAT_102

description:
SAT sample of Morbidly patient
5822791001_R05C02


title: Liver_77

description:
Liver sample of Morbidly patient
5822943028_R04C02


title: Liver_128

description:
Liver sample of Morbidly patient
5822943019_R03C01


title: Liver_103

description:
Liver sample of Morbidly patient
5822943019_R05C02


title: Liver_119

description:
Liver sample of Morbidly patient
5822943019_R06C02


title: Liver_64

description:
Liver sample of Morbidly patient
5822943015_R05C01


title: Liver_96

description:
Liver sample of Morbidly patient
5822943019_R03C02


title: Liver_58

description:
Liver sample of Morbidly patient
5822943019_R05C01


title: Liver_83

description:
Liver sample of Morbidly patient
5822943014_R04C02


title: Liver_130

description:
Liver sample of Morbidly patient
5822943014_R02C01


title: Liver_61

description:
Liver sample of Morbidly patient
5822943028_R02C02


title: Liver_84

description:
Liver sample of Morbidly patient
5822943013_R05C01


title: Liver_41

description:
Liver sample of Morbidly patient
5822943013_R06C01


title: SAT_58

description:
SAT sample of Morbidly patient
5822791019_R03C01


title: A549-8 weeks-2-rep 2

city: Maastricht

first: Simone

middle: G

last: van Breda

state: Limburg

address: Universiteitssingel 50

department: Toxicogenomics

institute: Maastricht University

description: Sample name: 8-2.0-R-2a

hyb_protocol: cRNA targets were hybridized on high-density oligonucleotide gene chips (Affymetrix Human Genome U133 Plus 2.0 GeneChip arrays) according to the Affymetrix Eukaryotic Target  hybridization manual. The gene chips were washed and stained using the Affymetrix Fluidics Station 450/250 and Genechip Operating Software

scan_protocol: Chips were scanned by means of an Affymetrix GeneArray scanner

data_processing: The Affymetrix CEL files were imported into R v2.15.0 [24] using the “affy” library within BioConductor (v2.9). Probesets were reannotated to EntrezGene genes using the BrainArray custom CDF v15.0 annotations. The quality of the arrays was assessed through box plots, fitPLM, NUSE, RLE, clustering/heat maps, PCA and correlation plots. No technically deviating arrays were detected. Probeset intensities were normalized using the RMA algorithm. For detecting differentially expressed genes, the “limma” library was used to construct a linear model containing coefficients for all factor combinations. The resulting p-values were FWER-corrected using the False Discovery Rate (FDR) approach.

label: Biotin

source_name: RNA from A549 cells exposed to 2 µM of sodium arsenite for 8 weeks replicate 2

label_protocol: cDNA was prepared using the Affymetrix One-Cycle cDNA synthesis kit (Affymetrix, Santa Clara). cDNA synthesis and labeling was performed according to the manufacturer’s  rocedures. Subsequent labeling of the samples was conducted by synthesis of Biotin-labeled complementary RNA (cRNA) using the GeneChip IVT labeling kit (Affymetrix). Purified cRNA was quantified using a spectrophotometer, and unfragmented samples were checked on the Bioanalyzer. Subsequently, cRNA samples were fragmented for target preparation according to the Affymetrix manual and checked on the Bioanalyzer.Samples were stored at  20 C until ready to perform hybridization.  cDNA synthesis kit (Affymetrix, Santa Clara). cDNA synthesis and labeling was  performed according to the manufacturer’s procedures. Subsequent labeling of  the samples was conducted by synthesis of Biotin-labeled complementary RNA  (cRNA) using the GeneChip IVT labeling kit (Affymetrix). Purified cRNA was  quantified using a spectrophotometer, and unfragmented samples were checked  on the Bioanalyzer. Subsequently, cRNA samples were fragmented for target  preparation according to the Affymetrix manual and checked on the Bioanalyzer.  Samples were stored at  20 C until ready to perform hybridization.

growth_protocol: A549 cells (human epithelial lung carcinoma cells; obtained from the American Type Culture Collection, Manassas, VA) were cultured in Dulbecco's modified Eagle's medium (Sigma) supplemented with 10% heat-inactivated fetal calf serum (Invitrogen) and 1% penicillin/streptomycin (Sigma) and maintained at 37 °C in a 5% CO2 atmosphere. Cells were seeded at a concentration of 4000 cells/cm2 in T25 flasks and trypsinized weekly.

extract_protocol: After removal of the medium, cells were lysed with TRIzol (Invitrogen) and total RNA was extracted using 0.5 ml TRIzol according to the manufacturer’s instructions. RNeasy Mini Kits (Qiagen, Westburg bv, The Netherlands) were used to purify total RNA from salts and residual DNA. From each sample, RNA quantity was measured spectrophotometrically using the NanoDrop 1000, and integrity was determined using the Bioanalyzer (Agilent Technologies, Amstelveen, the Netherlands). All samples had on OD 260/280 ratio between 1.8 and 2.0, and held an RNA integrity number > 8.

treatment_protocol: Cells were exposed to sodium arsenite (NaAsO2, Sigma) at concentrations of 0.08 µM, 0.4 µM and 2 µM for 1, 2 and 8 weeks. Exposure to sodium arsenite started 6 hours after the cells were seeded into the culture flasks to ensure that sodium arsenite did not affect attachment. The final concentrations of sodium arsenite were obtained by the appropriate dilution with media. Medium was changed after three days thereby providing a new dose of sodium arsenite to the cells. All experiments were performed in duplicate.

tag: cell type

value: A549 human epithelial lung carcinoma cells

tag: treatment

value: 2 µM of sodium arsenite

tag: time

value: 8 weeks


title: A549-8 weeks-2-rep 1

description: Sample name: 8-2.0-R-1a

source_name: RNA from A549 cells exposed to 2 µM of sodium arsenite for 8 weeks replicate 1


title: Liver_97

description:
Liver sample of Morbidly patient
5822943002_R03C01


title: SAT_87

description:
SAT sample of Morbidly patient
5822791011_R04C02


title: A549-8 weeks-0.4-rep 2

description: Sample name: 8-0.4-R-2a

source_name: RNA from A549 cells exposed to 0.4 µM of sodium arsenite for 8 weeks replicate 2

value: 0.4 µM of sodium arsenite


title: Liver_102

description:
Liver sample of Morbidly patient
5822943002_R01C01


title: Liver_106

description:
Liver sample of Morbidly patient
5822943002_R04C02


title: Liver_79

description:
Liver sample of Morbidly patient
5822943002_R05C01


title: Liver_52

description:
Liver sample of Morbidly patient
5822943013_R04C01


title: A549-8 weeks-0.4-rep 1

description: Sample name: 8-0.4-R-1a

source_name: RNA from A549 cells exposed to 0.4 µM of sodium arsenite for 8 weeks replicate 1


title: A549-8 weeks-0.08-rep 2

description: Sample name: 8-0.08-R-2a

source_name: RNA from A549 cells exposed to 0.08 µM of sodium arsenite for 8 weeks replicate 2

value: 0.08 µM of sodium arsenite


title: Liver_86

description:
Liver sample of Morbidly patient
5822943002_R03C02


title: Liver_37

description:
Liver sample of Morbidly patient
5822791030_R04C02


title: Liver_125

description:
Liver sample of Morbidly patient
5822943002_R04C01


title: SAT_130

description:
SAT sample of Morbidly patient
5822791013_R04C02


title: A549-8 weeks-0-rep 2

description: Sample name: 8-0-R-2a

source_name: RNA from A549 cells exposed to zero dose of sodium arsenite for 8 weeks replicate 2

value: zero dose of sodium arsenite


title: Liver_74

description:
Liver sample of Morbidly patient
5822791029_R05C01


title: A549-8 weeks-0-rep 1

description: Sample name: 8-0-R-1a

source_name: RNA from A549 cells exposed to zero dose of sodium arsenite for 8 weeks replicate 1


title: Liver_100

description:
Liver sample of Morbidly patient
5822791028_R06C01


title: A549-2 weeks-2-rep 2

description: Sample name: 2-2.0-R-2a

source_name: RNA from A549 cells exposed to 2 µM of sodium arsenite for 2 weeks replicate 2

value: 2 weeks


title: Liver_85

description:
Liver sample of Morbidly patient
5822791027_R04C01


title: Liver_68

description:
Liver sample of Morbidly patient
5822791028_R06C02


title: Liver_87

description:
Liver sample of Morbidly patient
5822791028_R05C02


title: A549-2 weeks-0.4-rep 2

description: Sample name: 2-0.4-R-2a

source_name: RNA from A549 cells exposed to 0.4 µM of sodium arsenite for 2 weeks replicate 2


title: Liver_92

description:
Liver sample of Morbidly patient
5822791028_R03C02


title: Liver_99

description:
Liver sample of Morbidly patient
5822791028_R01C02


title: Liver_78

description:
Liver sample of Morbidly patient
5822791027_R06C02


title: Liver_45

description:
Liver sample of Morbidly patient
5822791026_R03C01


title: Liver_54

description:
Liver sample of Morbidly patient
5822791026_R04C01


title: Liver_88

description:
Liver sample of Morbidly patient
5822791028_R04C01


title: Liver_127

description:
Liver sample of Morbidly patient
5822791024_R05C01


title: A549-8 weeks-0.08-rep 1

description: Sample name: 8-0.08-R-1a

source_name: RNA from A549 cells exposed to 0.08 µM of sodium arsenite for 8 weeks replicate 1


title: Liver_104

description:
Liver sample of Morbidly patient
5822791018_R04C02


title: Liver_114

description:
Liver sample of Morbidly patient
5822791018_R05C02


title: Liver_113

description:
Liver sample of Morbidly patient
5822943028_R03C01


title: A549-2 weeks-0.08-rep 2

description: Sample name: 2-0.08-R-2a

source_name: RNA from A549 cells exposed to 0.08 µM of sodium arsenite for 2 weeks replicate 2


title: A549-2 weeks-0.4-rep 1

description: Sample name: 2-0.4-R-1a

source_name: RNA from A549 cells exposed to 0.4 µM of sodium arsenite for 2 weeks replicate 1


title: SAT_69

description:
SAT sample of Morbidly patient
5822791019_R01C02


title: A549-2 weeks-2-rep 1

description: Sample name: 2-2.0-R-1a

source_name: RNA from A549 cells exposed to 2 µM of sodium arsenite for 2 weeks replicate 1


title: Liver_93

description:
Liver sample of Morbidly patient
5822791015_R05C01


title: Liver_75

description:
Liver sample of Morbidly patient
5822791019_R03C02


title: Liver_53

description:
Liver sample of Morbidly patient
5822791019_R06C01


title: Liver_48

description:
Liver sample of Morbidly patient
5822791029_R04C01


title: A549-2 weeks-0-rep 2

description: Sample name: 2-0-R-2a

source_name: RNA from A549 cells exposed to zero dose of sodium arsenite for 2 weeks replicate 2


title: A549-1 week-0.4-rep 1

description: Sample name: 1-0.4-R-1a

source_name: RNA from A549 cells exposed to 0.4 µM of sodium arsenite for 1 week replicate 1

value: 1 week


title: A549-1 week-2-rep 2

description: Sample name: 1-2.0-R-2a

source_name: RNA from A549 cells exposed to 2 µM of sodium arsenite for 1 week replicate 2


title: A549-1 week-2-rep 1

description: Sample name: 1-2.0-R-1a

source_name: RNA from A549 cells exposed to 2 µM of sodium arsenite for 1 week replicate 1


title: A549-2 weeks-0-rep 1

description: Sample name: 2-0-R-1a

source_name: RNA from A549 cells exposed to zero dose of sodium arsenite for 2 weeks replicate 1


title: A549-1 week-0.4-rep 2

description: Sample name: 1-0.4-R-2a

source_name: RNA from A549 cells exposed to 0.4 µM of sodium arsenite for 1 week replicate 2


title: Liver_89

description:
Liver sample of Morbidly patient
5822791015_R03C02

source_name: severely obese patient_liver


title: Liver_95

description:
Liver sample of Morbidly patient
5822791015_R05C02


title: A549-1 week-0.08-rep 2

description: Sample name: 1-0.08-R-2a

source_name: RNA from A549 cells exposed to 0.08 µM of sodium arsenite for 1 week replicate 2


title: A549-2 weeks-0.08-rep 1

description: Sample name: 2-0.08-R-1a

source_name: RNA from A549 cells exposed to 0.08 µM of sodium arsenite for 2 weeks replicate 1


title: A549-1 week-0-rep 2

description: Sample name: 1-0-R-2a

source_name: RNA from A549 cells exposed to zero dose of sodium arsenite for 1 week replicate 2


title: A549-1 week-0.08-rep 1

description: Sample name: 1-0.08-R-1a

source_name: RNA from A549 cells exposed to 0.08 µM of sodium arsenite for 1 week replicate 1


title: A549-1 week-0-rep 1

description: Sample name: 1-0-R-1a

source_name: RNA from A549 cells exposed to zero dose of sodium arsenite for 1 week replicate 1


title: Liver_55

description:
Liver sample of Morbidly patient
5822791013_R05C01


title: Liver_73

description:
Liver sample of Morbidly patient
5822791013_R02C01


title: Liver_116

description:
Liver sample of Morbidly patient
5822791012_R04C02


title: Liver_120

description:
Liver sample of Morbidly patient
5822791012_R03C02


title: csrAvsYPIII_FLUX_GEO_sample02

city: Braunschweig

first: Ann

middle: Kathrin

last: Heroven

state: Niedersachsen

address: Inhoffenstr. 7

department: Molecular Infection Biology

country: Germany

institute: Helmholtz Centre for Infection Research

description: Biological replicate 2 of 3.

hyb_protocol: 300ng of each Cy3- and Cy5-labelled RNA and hybridized to the microarray at 65°C for 17 hours using the Agilent Hybridization Chamber according to the Agilent instructions

scan_protocol: The array were scanned at a resolution of 5μm using the Axon GenePix Personal 4100A microarray scanner (Axon instruments) and features were extracted using GenePix Pro 6

data_processing: For feature extraction the software Feature Extraction 10.7.3.1 (Agilent Technologies, USA) was used, data processing was carried out using the Bioconducter – Linear Models for Microarray analysis (LIMMA) package of the R language (http://www.r-project.org).

organism: Yersinia pseudotuberculosis

source_name: Yersinia pseudotuberculosis wild type exponential phase culture grown in Yersinia minimal medium at 25°C

label_protocol: RNA samples were labelled either with Cy3 (mutant) or Cy5 (wild type) using the ULS fluorescent labelling kit (Kreatech, Germany)

growth_protocol: Y. pseudotuberculosis YPIII or the isogenic csrA mutant strain were cultivated at 25°C under aeration on a rotary shaker. First pre-cultures were grown in a 1:1 mixture of HAM’s F-12 Nutrient Mixture (Invitrogen, Carlsbad, US) and liquid DMEM medium (Biochrom, Berlin, DE). Second pre-cultures and main cultures were grown in a Yersinia minimal medium (YMM), which was developed in the present work. It contained per liter: 8 g glucose, 6.62 g KH2PO4, 13.26 g K2HPO4, 0.31 g NaCl, 5 g (NH4)2SO4, 0.20 g MgSO4∙7H2O, 30 mg 3,4-dihydroxybenzoic acid, 0.5 mg FeSO4∙7H2O, 0.5 mg ZnSO4∙7H2O, 2 mg FeCl3∙6H2O, 2 mg MnSO4∙H2O, 0.8 mg ZnSO4∙7H2O, 0.2 mg CuCl2∙2H2O, 0.2 mg Na2B4O7∙10H2O and 0.1 mg (NH4)6Mo7O24∙4H2O. The analysis comprised three biological replicates for each strain. In addition, samples, taken at three different time points of the exponential growth phase, were used to validate constant expression during the cultivation.

extract_protocol: RNA extraction was performed using the SV Total RNA Isolation System (Promega)

tag: strain

value: YPIII pIB1 wild type

source_name: Yersinia pseudotuberculosis csrA mutant exponential phase culture grown in Yersinia minimal medium at 25°C

value: YPIII pIB1 csrA mutant; YP53


title: rovAvsYPIII_FLUX_GEO_sample03

description: Biological replicate 3 of 3.

growth_protocol: Y. pseudotuberculosis YPIII or the isogenic rovA mutant strain were cultivated at 25°C under aeration on a rotary shaker. First pre-cultures were grown in a 1:1 mixture of HAM’s F-12 Nutrient Mixture (Invitrogen, Carlsbad, US) and liquid DMEM medium (Biochrom, Berlin, DE). Second pre-cultures and main cultures were grown in a Yersinia minimal medium (YMM), which was developed in the present work. It contained per liter: 8 g glucose, 6.62 g KH2PO4, 13.26 g K2HPO4, 0.31 g NaCl, 5 g (NH4)2SO4, 0.20 g MgSO4∙7H2O, 30 mg 3,4-dihydroxybenzoic acid, 0.5 mg FeSO4∙7H2O, 0.5 mg ZnSO4∙7H2O, 2 mg FeCl3∙6H2O, 2 mg MnSO4∙H2O, 0.8 mg ZnSO4∙7H2O, 0.2 mg CuCl2∙2H2O, 0.2 mg Na2B4O7∙10H2O and 0.1 mg (NH4)6Mo7O24∙4H2O. The analysis comprised three biological replicates for each strain. In addition, samples, taken at three different time points of the exponential growth phase, were used to validate constant expression during the cultivation.

source_name: Yersinia pseudotuberculosis rovA mutant exponential phase culture grown in Yersinia minimal medium at 25°C

value: YPIII pIB1 rovA mutant; YP3


title: csrAvsYPIII_FLUX_GEO_sample03

description: Biological replicate 3 of 3.


title: rovAvsYPIII_FLUX_GEO_sample01

description: Biological replicate 1 of 3.


title: csrAvsYPIII_FLUX_GEO_sample01

description: Biological replicate 1 of 3.


title: rovAvsYPIII_FLUX_GEO_sample02

description: Biological replicate 2 of 3.


title: crpvsYPIII_FLUX_GEO_sample03

description: Biological replicate 3 of 3.

growth_protocol: Y. pseudotuberculosis YPIII or the isogenic crp mutant strain were cultivated at 25°C under aeration on a rotary shaker. First pre-cultures were grown in a 1:1 mixture of HAM’s F-12 Nutrient Mixture (Invitrogen, Carlsbad, US) and liquid DMEM medium (Biochrom, Berlin, DE). Second pre-cultures and main cultures were grown in a Yersinia minimal medium (YMM), which was developed in the present work. It contained per liter: 8 g glucose, 6.62 g KH2PO4, 13.26 g K2HPO4, 0.31 g NaCl, 5 g (NH4)2SO4, 0.20 g MgSO4∙7H2O, 30 mg 3,4-dihydroxybenzoic acid, 0.5 mg FeSO4∙7H2O, 0.5 mg ZnSO4∙7H2O, 2 mg FeCl3∙6H2O, 2 mg MnSO4∙H2O, 0.8 mg ZnSO4∙7H2O, 0.2 mg CuCl2∙2H2O, 0.2 mg Na2B4O7∙10H2O and 0.1 mg (NH4)6Mo7O24∙4H2O. The analysis comprised three biological replicates for each strain. In addition, samples, taken at three different time points of the exponential growth phase, were used to validate constant expression during the cultivation.

source_name: Yersinia pseudotuberculosis crp mutant exponential phase culture grown in Yersinia minimal medium at 25°C

value: YPIII pIB1 crp mutant; YP89


title: crpvsYPIII_FLUX_GEO_sample01

description: Biological replicate 1 of 3.


title: Liver_62

description:
Liver sample of Morbidly patient
5822791011_R05C02

value: severely obese patient


title: crpvsYPIII_FLUX_GEO_sample02

description: Biological replicate 2 of 3.


title: Liver_124

description:
Liver sample of Morbidly patient
5822791012_R02C02

value: male


title: Liver_76

description:
Liver sample of Morbidly patient
5822791013_R06C01

value: female


title: Liver_69

description:
Liver sample of Morbidly patient
5822791011_R05C01


title: Sirolimus NW_117

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

source_name: Kidney biopsies from transplant recipients treated with Sirolimus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip® Expression Analysis Technical Manual, Affymetrix).

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

value: peripheral blood

value: Sirolimus


title: Ciprofloxacin (CPFX) resistant strain_Line3

city: Suita

first: Chikara

last: Furusawa

state: Osaka

address: 6-2-3 Furuedai

department: Quantitative Biology Center (QBiC)

country: Japan

institute: RIKEN

hyb_protocol: After confirmation of yields (> 825 ng) and specific activities (> 15 pmol/μg) of the Cy3-labbeled cRNAs using NanoDrop ND-2000, 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to custom designed the Agilent 8× 60K arrays for E. coli W3110, E.coli_K12_Expression_Ver.1, for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (AgilentG3_GX_1Color, Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: ExternalFullGEML_043017_D_F_20120907) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Escherichia coli

source_name: Exponential culture of CPFX resistant strain Line3

label_protocol: One hundred ng of purified total RNAs was labeled using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies) with Cyanine3 (Cy3) in accordance with the manufacturer’s instructions.

growth_protocol: Precultures were prepared by shaking -80 °C glycerol stocked parent and evolved resistant strains in 200 uL of modified M9 medium in 96-well microplates for 23 h at 34 °C without antibiotic. The cells precultured were diluted to an OD600 nm of 1　× 10^-4 into 200 uL of fresh modified M9 medium in 96-well microplates. Then, cultures were grown with shaking at 34 °C to an OD600 in the 0.072 ~ 0.135 range (equivalent of 10 generations).

extract_protocol: Total RNA was isolated and purified from cells using an RNeasy micro kit with on-column DNA digestion (Qiagen) in accordance with the manufacturer’s instructions. The quality of the purified RNA was evaluated using Agilent 2100 Bioanalyzer with an RNA 6000 Nano kit (Agilent Technologies). Only purified RNAs that had RIN (RNA integrity number) of 9.0 or more were utilized. The purified RNAs were stored at −80°C prior to transcriptome analysis.

treatment_protocol: One hundred eighty uL of exponential cultures were withdrawn rapidly, and cells were killed immediately by the addition of an equal volume of ice-cold ethanol that contained 10% (w/v) phenol. The cells were collected by centrifugation at 20,000　× g at 4 °C for 5 min, and the pelleted cells were stored at −80 °C prior to RNA extraction.

value: Ciprofloxacin (CPFX) resistant strain Line3


title: Ciprofloxacin (CPFX) resistant strain_Line4

source_name: Exponential culture of CPFX resistant strain Line4

value: Ciprofloxacin (CPFX) resistant strain Line4


title: Sirolimus NW_110


title: Sirolimus NW_112


title: Sirolimus NW_109


title: Sirolimus NW_95


title: Ciprofloxacin (CPFX) resistant strain_Line1

source_name: Exponential culture of CPFX resistant strain Line1

value: Ciprofloxacin (CPFX) resistant strain Line1


title: Ciprofloxacin (CPFX) resistant strain_Line2

source_name: Exponential culture of CPFX resistant strain Line2

value: Ciprofloxacin (CPFX) resistant strain Line2


title: Liver_66

description:
Liver sample of Morbidly patient
5822791008_R01C01

value: liver


title: Liver_36

description:
Liver sample of Morbidly patient
5822791011_R02C01


title: Liver_112

description:
Liver sample of Morbidly patient
5822791003_R06C02


title: Liver_43

description:
Liver sample of Morbidly patient
5822791008_R01C02


title: Enoxacin (ENX) resistant strain_Line4

source_name: Exponential culture of ENX resistant strain Line4

value: Enoxacin (ENX) resistant strain Line4


title: Liver_110

description:
Liver sample of Morbidly patient
5822791008_R02C02


title: Sirolimus NW_82


title: Liver_51

description:
Liver sample of Morbidly patient
5822791011_R01C01


title: Liver_91

description:
Liver sample of Morbidly patient
5822791002_R02C02


title: Liver_90

description:
Liver sample of Morbidly patient
5822791012_R04C01


title: Liver_71

description:
Liver sample of Morbidly patient
5822791001_R04C01


title: Enoxacin (ENX) resistant strain_Line3

source_name: Exponential culture of ENX resistant strain Line3

value: Enoxacin (ENX) resistant strain Line3


title: Enoxacin (ENX) resistant strain_Line2

source_name: Exponential culture of ENX resistant strain Line2

value: Enoxacin (ENX) resistant strain Line2


title: Liver_131

description:
Liver sample of Morbidly patient
5822791013_R05C02

source_name: severely obese patient_liver


title: Enoxacin (ENX) resistant strain_Line1

source_name: Exponential culture of ENX resistant strain Line1

value: Enoxacin (ENX) resistant strain Line1


title: Sirolimus NW_81


title: Liver_42

description:
Liver sample of Morbidly patient
5822791003_R03C02


title: Liver_40

description:
Liver sample of Morbidly patient
5822791003_R03C01


title: Liver_123

description:
Liver sample of Morbidly patient
5822791001_R02C02


title: Liver_107

description:
Liver sample of Morbidly patient
5822791001_R01C01


title: Trimethoprim (TP) resistant strain_Line2

source_name: Exponential culture of TP resistant strain Line2

value: Trimethoprim (TP) resistant strain Line2


title: Trimethoprim (TP) resistant strain_Line4

source_name: Exponential culture of TP resistant strain Line4

value: Trimethoprim (TP) resistant strain Line4


title: Trimethoprim (TP) resistant strain_Line3

source_name: Exponential culture of TP resistant strain Line3

value: Trimethoprim (TP) resistant strain Line3


title: Sirolimus NW_100


title: Trimethoprim (TP) resistant strain_Line1

source_name: Exponential culture of TP resistant strain Line1

value: Trimethoprim (TP) resistant strain Line1


title: Sirolimus NW_80


title: Sirolimus NW_56


title: Liver_63

description:
Liver sample of Morbidly patient
5822791001_R02C01

value: severely obese patient


title: Sirolimus NW_47


title: Sirolimus NW_78


title: Sirolimus NW_68


title: Day 28_TC rep2

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

description:
replicate 2
4256265088_E

hyb_protocol: cDNA was synthesized using Illumina RNA Amplification Kit and hybridized to Illumina Mouse-6 v1.1 BeadChip microarrays according to manufacturer's instructions.

scan_protocol: Bead array (Illumina)

data_processing: Illumina BeadStudio extracted gene expression intensities were background corrected and quantile normalized using Lumi v2.10 (Bioconductor v2.18, R v2.15.3).

source_name: EGFP+ tissue capsule cell, day 28,rep2

label_protocol: Biotin-labeled amplified mRNA (aRNA) was synthesized with the Illumina RNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: Sterile foreign objects  were inserted into the peritoneal cavities of MacGreen mice (in which the Csf1r promoter directs myeloid-specific EGFP expression).  At various time-points post-surgery (days 2, 4, 7, 14), mice were euthanased, and peritoneal exudate cells collecteded by lavage.  Peritoneal exudate cells from MacGreen mice that had not received implants were used as controls (day 0; 'unstimulated').  Free-floating objects encapsulated with tissue were removed from the peritoneal cavities of different mice at days 7, 14, 21, 28.

extract_protocol: Total RNA from pooled FACS-sorted EGFPhi peritoneal exudate and tissue capsule cells was obtained using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.  RNA quality was analysed for quality by Bioanalyser (Agilent, Santa Clara, CA) and quantity by spectrophotometer (ND-1000; Thermo Scientific, Waltham, MA).

treatment_protocol: Peritoneal exudate cells obtained by lavage, and single cell suspensions obtained by collagenase digestion of tissue capsules, were separated on the basis of size/granularity and EGFP  fluorescence.

value: sterile foreign object

value: Day 28

value: peritoneal myeloid cells

value: 10-16 weeks


title: Sirolimus NW_111

value: peripheral blood

value: Sirolimus


title: Liver_122

description:
Liver sample of Morbidly patient
5822791003_R04C01

value: female


title: Day 21_TC rep2

description:
replicate 2
4256265088_C

source_name: EGFP+ tissue capsule cell, day 21,rep2

value: Day 21


title: Day 28_TC rep1

description:
replicate 1
4256265088_D

source_name: EGFP+ tissue capsule cell, day 28,rep1


title: Day 14_TC rep2

description:
replicate 2
4112157060_B

source_name: EGFP+ tissue capsule cell, day 14,rep2

value: Day 14


title: Day 7_TC rep2

description:
replicate 2
4090066029_F

source_name: EGFP+ tissue capsule cell, day 7,rep2

value: Day 7


title: Azithromycin (AZM) resistant strain_Line3

source_name: Exponential culture of AZM resistant strain Line3

value: Azithromycin (AZM) resistant strain Line3


title: Sirolimus NW_35

source_name: Kidney biopsies from transplant recipients treated with Sirolimus


title: Day 21_TC rep1

description:
replicate 1
4256265088_B

source_name: EGFP+ tissue capsule cell, day 21,rep1


title: Azithromycin (AZM) resistant strain_Line2

source_name: Exponential culture of AZM resistant strain Line2

value: Azithromycin (AZM) resistant strain Line2


title: Sirolimus NW_36


title: Sirolimus NW_44


title: Day 14_TC rep1

description:
replicate 1
4112157060_A

source_name: EGFP+ tissue capsule cell, day 14,rep1


title: Day 2_L rep2

description:
replicate 2
4090066029_B

source_name: EGFP+ peritoneal lavage cells, day 2,rep2

value: Day 2


title: Sirolimus NW_23


title: Azithromycin (AZM) resistant strain_Line4

source_name: Exponential culture of AZM resistant strain Line4

value: Azithromycin (AZM) resistant strain Line4


title: Day 7_L rep2

description:
replicate 2
4090066029_D

source_name: EGFP+ peritoneal lavage cells, day 7,rep2


title: Day 4_L rep2

description:
replicate 2
4090066029_C

source_name: EGFP+ peritoneal lavage cells, day 4,rep2

value: Day 4


title: Day 14_L rep2

description:
replicate 2
4090066029_E

source_name: EGFP+ peritoneal lavage cells, day 14,rep2


title: Day 0_L rep2

description:
replicate 2
4090066029_A

source_name: EGFP+ peritoneal lavage cells, day 0,rep2

value: control

value: Day 0


title: Day 7_TC rep1

description:
replicate 1
4090066028_F

source_name: EGFP+ tissue capsule cell, day 7,rep1

value: sterile foreign object


title: Chloramphenicol (CP) resistant strain_Line3

source_name: Exponential culture of CP resistant strain Line3

value: Chloramphenicol (CP) resistant strain Line3


title: Chloramphenicol (CP) resistant strain_Line4

source_name: Exponential culture of CP resistant strain Line4

value: Chloramphenicol (CP) resistant strain Line4


title: Chloramphenicol (CP) resistant strain_Line2

source_name: Exponential culture of CP resistant strain Line2

value: Chloramphenicol (CP) resistant strain Line2


title: Chloramphenicol (CP) resistant strain_Line1

source_name: Exponential culture of CP resistant strain Line1

value: Chloramphenicol (CP) resistant strain Line1


title: Azithromycin (AZM) resistant strain_Line1

source_name: Exponential culture of AZM resistant strain Line1

value: Azithromycin (AZM) resistant strain Line1


title: CMPs from CEBPa KO mouse BM, rep3

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed using RMA in the bioconducter and normalized using the Cross Correlation method.  The trimmed mean target intensity of each array was set to 8 (3 in log2 scale).

source_name: CMPs (#3) from CEBPa KO mouse bone marrow, 5 days after 3xPIPC

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

growth_protocol: Hematopoietic Stem Cell enriched Lin-Sca-1+c-kit+ cells (KSLs) and their downstream common myeloid progenitors (CMPs: Lin-c-kit+Sca1-CD34+FcrRII/III-) were isolated from poly(inosinic acid) poly(cytidylic acid) (Poly I:C) treated (3 times, every other day) Mx.1-Cre- C/EBPa f/f control (Ctl) and Mx.1-Cre+ C/EBPaf/f C/EBPa conditional knockout (KO) mouse bone marrow and cultured in serum-free StemSpan SFEM medium (Stem Cell Technologies) containing 100ng/ml mSCF, 100ng/ml mTPO, and 10ng/ml mIl-3.

extract_protocol: Cell were extracted using NuGen Ovation Pico WTA system V2. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: C/EBPa Ctl or KO KSLs or CMPs were infected with MSCV-MLL-AF9-IRES-GFP retrovirus and transplanted into lethally irradiated congenic recipients along with 2x105 congenic bone marrow cells for radioprotection. To develop C/EBPa independent MF9 induced leukemic, KO-MF9 recipients were injected with 1 mg IL-3 and GM-CSF expressing vectors using a hydrodynamic-based method 2-4 months after transplantation.

value: CMPs

tag: source

value: CEBPa KO mouse bone marrow


title: Day 4_L rep1

description:
replicate 1
4090066028_C

source_name: EGFP+ peritoneal lavage cells, day 4,rep1

value: peritoneal myeloid cells

value: 10-16 weeks


title: CMPs from CEBPa KO mouse BM, rep4

source_name: CMPs (#4) from CEBPa KO mouse bone marrow, 5 days after 3xPIPC


title: Day 7_L rep1

description:
replicate 1
4090066028_D

source_name: EGFP+ peritoneal lavage cells, day 7,rep1

value: Day 7


title: Doxycycline (DOXY) resistant strain_Line4

source_name: Exponential culture of DOXY resistant strain Line4

value: Doxycycline (DOXY) resistant strain Line4


title: CMPs from CEBPa KO mouse BM, rep1

source_name: CMPs (#1) from CEBPa KO mouse bone marrow, 5 days after 3xPIPC


title: Day 0_L rep1

description:
replicate 1
4090066028_A

source_name: EGFP+ peritoneal lavage cells, day 0,rep1


title: CMPs from CEBPa KO mouse BM, rep2

source_name: CMPs (#2) from CEBPa KO mouse bone marrow, 5 days after 3xPIPC


title: Lung_CNT-1, 90days

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

institute: National Institute of Advanced Industrial Science and Technology

description:
Gene expression after 90 days in CNT-1-instilled rat lungs
CN500_52

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan resolution 5um).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014879_D_F_20110906). Background detrend: On (Feat NCRange, LoPass). Multiplicative detrend: True. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalized data is the average of n=4 (CN200_004: N=3).

source_name: Rat lungs, 90 days, CNT-1, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Tokyo, Japan). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Nine-week-old male Wistar rats purchased from Japan SLC, Inc. (Shizuoka, Japan) were divided into groups (n = 4 per group per time point). CNT-1 or CNT-2 were intratracheally administered into rats as a single injection (0.4 mg SWCNTs per rat). The vehicle control groups received  1.0mg/mL BSA per rat. After intratracheal instillation treatment, rats were housed within polycarbonate cages at a controlled temperature of 22 ◦C with a chow diet ad libitum, and were dissected at 1day, 3 days, 7 days, 30 days, and 90 days post-instillation. Lungs of anesthetized rats were perfused with physiological saline, excised, and used for the morphological observation, histopathological findings, the bronchoalveolar lavage fluid (BALF) analysis, cytokine assay and comprehensive gene expression analysis. All procedures and animal handling were performed by Public Interest Incorporated Foundation, Biosafety Research Center (BSRC), Shizuoka, Japan according to the guidelines described in the Japanese Guide for the Care and Use of Laboratory Animals as approved by the Animal Care and Use Committee.

extract_protocol: The right lungs (n = 4 per group per time point) were homogenized using QIAzol lysis reagent with a Tissue Ruptor (Qiagen, Tokyo, Japan). Total RNA from the homogenates was extracted using the RNeasy Midi kit (Qiagen) following the manufacturer’s instructions. RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, US) and the quality of the samples was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, US).

treatment_protocol: 0.4 mg of CNT-1 or CNT-2 was suspended in 0.4 ml of 1.0mg/mL BSA. Each material suspension was intratracheally instilled once in rats. The animals were dissected at 1day, 3 days, 7 days, 30 days, and 90 days after instillation.

value: Wistar

value: nine-weeks-old

value: male

tag: time (post-instillation period)

value: 90 days

value: right lung


title: Day 2_L rep1

description:
replicate 1
4090066028_B

source_name: EGFP+ peritoneal lavage cells, day 2,rep1

value: sterile foreign object

value: Day 2

tag: age


title: Lung_Control, 90days

description:
Gene expression after 90 days in vehicle control-instilled rat lungs
CN500_51

source_name: Rat lungs, 90 days, Vehicle control, replicate 4

value: vehicle control-instilled


title: CMPs from CEBPa control mouse BM, rep4

source_name: CMPs (#4) from CEBPa wt control mouse bone marrow, 5 days after 3xPIPC

value: CEBPa wt control mouse bone marrow


title: Lung_CNT-2, 90days

description:
Gene expression after 90 days in CNT-2-instilled rat lungs
CN500_53

source_name: Rat lungs, 90 days, CNT-2, replicate 4


title: Day 14_L rep1

description:
replicate 1
4090066028_E

source_name: EGFP+ peritoneal lavage cells, day 14,rep1

value: Day 14


title: Lung_Control, 30days

description:
Gene expression after 30 days in vehicle control-instilled rat lungs
CN500_41

source_name: Rat lungs, 30 days, Vehicle control, replicate 4

value: 30 days


title: GMPs from CEBPa control mouse BM, rep2

source_name: GMPs (#2) from CEBPa wt control mouse bone marrow, 5 days after 3xPIPC

value: GMPs


title: Lung_CNT-1, 30days

description:
Gene expression after 30 days in CNT-1-instilled rat lungs
CN500_42

source_name: Rat lungs, 30 days, CNT-1, replicate 4


title: Doxycycline (DOXY) resistant strain_Line3

source_name: Exponential culture of DOXY resistant strain Line3

value: Doxycycline (DOXY) resistant strain Line3


title: Lung_CNT-2, 7days

description:
Gene expression after 7 days in CNT-2-instilled rat lungs
CN500_33

source_name: Rat lungs, 7 days, CNT-2, replicate 4

value: 7 days


title: GMPs from CEBPa control mouse BM, rep3

source_name: GMPs (#3) from CEBPa wt control mouse bone marrow, 5 days after 3xPIPC


title: GMPs from CEBPa control mouse BM, rep1

source_name: GMPs (#1) from CEBPa wt control mouse bone marrow, 5 days after 3xPIPC


title: Doxycycline (DOXY) resistant strain_Line1

source_name: Exponential culture of DOXY resistant strain Line1

value: Doxycycline (DOXY) resistant strain Line1


title: Lung_CNT-2, 30days

description:
Gene expression after 30 days in CNT-2-instilled rat lungs
CN500_43

source_name: Rat lungs, 30 days, CNT-2, replicate 4


title: Neomycin (NM) resistant strain_Line4

source_name: Exponential culture of NM resistant strain Line4

value: Neomycin (NM) resistant strain Line4


title: Doxycycline (DOXY) resistant strain_Line2

source_name: Exponential culture of DOXY resistant strain Line2

value: Doxycycline (DOXY) resistant strain Line2


title: Lung_CNT-1, 7days

description:
Gene expression after 7 days in CNT-1-instilled rat lungs
CN500_32

source_name: Rat lungs, 7 days, CNT-1, replicate 4

value: Wistar


title: Lung_CNT-2, 3days

description:
Gene expression after 3 days in CNT-2-instilled rat lungs
CN500_23

source_name: Rat lungs, 3 days, CNT-2, replicate 4

value: nine-weeks-old

value: 3 days


title: Lung_Control, 7days

description:
Gene expression after 7 days in vehicle control-instilled rat lungs
CN500_31

source_name: Rat lungs, 7 days, Vehicle control, replicate 4

value: male


title: Lung_CNT-1, 3days

description:
Gene expression after 3 days in CNT-1-instilled rat lungs
CN500_22

source_name: Rat lungs, 3 days, CNT-1, replicate 4

value: right lung


title: Neomycin (NM) resistant strain_Line3

source_name: Exponential culture of NM resistant strain Line3

value: Neomycin (NM) resistant strain Line3


title: Lung_Control, 3days

description:
Gene expression after 3 days in vehicle control-instilled rat lungs
CN500_21

source_name: Rat lungs, 3 days, Vehicle control, replicate 4


title: Lung_CNT-1, 1day

description:
Gene expression after 1 day in CNT-1-instilled rat lungs
CN500_12

source_name: Rat lungs, 1 day, CNT-1, replicate 4

value: 1 day


title: Neomycin (NM) resistant strain_Line1

source_name: Exponential culture of NM resistant strain Line1

value: Neomycin (NM) resistant strain Line1


title: Neomycin (NM) resistant strain_Line2

source_name: Exponential culture of NM resistant strain Line2

value: Neomycin (NM) resistant strain Line2


title: CMPs from CEBPa control mouse BM, rep2

source_name: CMPs (#2) from CEBPa wt control mouse bone marrow, 5 days after 3xPIPC

value: CMPs

value: CEBPa wt control mouse bone marrow


title: Amikacin (AMK) resistant strain_Line4

source_name: Exponential culture of AMK resistant strain Line4

value: Amikacin (AMK) resistant strain Line4


title: Lung_Control, 1day

description:
Gene expression after 1 day in vehicle control-instilled rat lungs
CN500_11

source_name: Rat lungs, 1 day, Vehicle control, replicate 4

value: vehicle control-instilled


title: CMPs from CEBPa control mouse BM, rep1

source_name: CMPs (#1) from CEBPa wt control mouse bone marrow, 5 days after 3xPIPC


title: CMPs from CEBPa control mouse BM, rep3

source_name: CMPs (#3) from CEBPa wt control mouse bone marrow, 5 days after 3xPIPC


title: Amikacin (AMK) resistant strain_Line3

source_name: Exponential culture of AMK resistant strain Line3

value: Amikacin (AMK) resistant strain Line3


title: Lung_CNT-2, 1day

description:
Gene expression after 1 day in CNT-2-instilled rat lungs
CN500_13

source_name: Rat lungs, 1 day, CNT-2, replicate 4


title: Amikacin (AMK) resistant strain_Line1

source_name: Exponential culture of AMK resistant strain Line1

value: Amikacin (AMK) resistant strain Line1


title: Amikacin (AMK) resistant strain_Line2

source_name: Exponential culture of AMK resistant strain Line2

value: Amikacin (AMK) resistant strain Line2


title: GFP+ CMPs from CEBPa KO-KSL-MLL-AF9 mouse BM, rep1

source_name: GFP+ CMPs isolated from CEBPa KO-KSL-MLL-AF9 mouse (091412#9) bone marrow

value: GFP+ CMPs


title: GFP+ CMPs from CEBPa KO-KSL-MLL-AF9 mouse BM, rep3

source_name: GFP+ CMPs isolated from CEBPa KO-KSL-MLL-AF9 mouse (091412#4) bone marrow


title: GFP+ CMPs from CEBPa KO-KSL-MLL-AF9 mouse BM, rep2

source_name: GFP+ CMPs isolated from CEBPa KO-KSL-MLL-AF9 mouse (091412#11) bone marrow


title: GFP+ KSLs from CEBPa KO-KSL-MLL-AF9 mouse BM, rep2

source_name: GFP+ KSLs isolated from CEBPa KO-KSL-MLL-AF9 mouse (091412#11) bone marrow

value: GFP+ KSLs


title: Cefixime (CFIX) resistant strain_Line3

source_name: Exponential culture of CFIX resistant strain Line3

value: Cefixime (CFIX) resistant strain Line3


title: Cefixime (CFIX) resistant strain_Line4

source_name: Exponential culture of CFIX resistant strain Line4

value: Cefixime (CFIX) resistant strain Line4


title: GFP+ KSLs from CEBPa KO-KSL-MLL-AF9 mouse BM, rep1

source_name: GFP+ KSLs isolated from CEBPa KO-KSL-MLL-AF9 mouse (091412#9) bone marrow


title: LGMPs from 2nd transplants with KO-MLL-AF9 mouse BM, rep2

source_name: LGMPs (#2) isolated from 2nd transplants with KO-MF9 il3+gm 100912 #3 bone marrow

value: LGMPs


title: LGMPs from 2nd transplants with KO-MLL-AF9 mouse BM, rep1

source_name: LGMPs (#1) isolated from 2nd transplants with KO-MF9 il3+gm 100912 #3 bone marrow


title: Cefixime (CFIX) resistant strain_Line2

source_name: Exponential culture of CFIX resistant strain Line2

value: Cefixime (CFIX) resistant strain Line2


title: Cefixime (CFIX) resistant strain_Line1

source_name: Exponential culture of CFIX resistant strain Line1

value: Cefixime (CFIX) resistant strain Line1


title: L-GMPs from CEBPa KO-KSL-MLL-AF9 mouse BM, rep1

source_name: GFP+ L-GMPs isolated from CEBPa KO-KSL-MLL-AF9 mouse (KO-MF9 il3+gm 100912 #3 L-GMP) bone marrow

value: GFP+ L-GMPs


title: L-GMPs from control-KSL-MLL-AF9 mouse BM, rep2

source_name: LGMPs (#2) isolated from control-KSL-MLL-AF9 mouse bone marrow

value: control-KSL-MLL-AF9 mouse bone marrow


title: LGMPs from 2nd transplants with control-MLL-AF9 mouse BM, rep 1

source_name: LGMPs (#1) isolated from 2nd transplants with control-MLL-AF9 mouse bone marrow

value: 2nd transplants with control-KSL-MLL-AF9 mouse bone marrow


title: Cefoperazone (CPZ) resistant strain_Line4

source_name: Exponential culture of CPZ resistant strain Line4

value: Cefoperazone (CPZ) resistant strain Line4


title: Cefoperazone (CPZ) resistant strain_Line3

source_name: Exponential culture of CPZ resistant strain Line3

value: Cefoperazone (CPZ) resistant strain Line3


title: L-GMPs from control-KSL-MLL-AF9 mouse BM, rep1

source_name: LGMPs (#1) isolated from control-KSL-MLL-AF9 mouse bone marrow


title: LGMPs from 2nd transplants with control-MLL-AF9 mouse BM, rep 2

source_name: LGMPs (#2) isolated from 2nd transplants with control-KSL-MLL-AF9 mouse bone marrow


title: Cefoperazone (CPZ) resistant strain_Line2

source_name: Exponential culture of CPZ resistant strain Line2

value: Cefoperazone (CPZ) resistant strain Line2


title: Parent strain_rep2

source_name: Exponential culture of the parent strain without antibiotic

value: Parent strain


title: tumor tissue

first: Yu

last: Shi

state: Chongqing

address: Gao-tan Yan Street

department: Southwest Hospital

institute: Institute of Pathology and Southwest Cancer Center

description:
GBM-T
Agilent's microRNA Spike- In kit consists of two microRNA Spike-In solutions for process control.

hyb_protocol: Each of the labeled samples were combined with Agilent 10x Blocking Agent and Agilent 2x Hi-RPM Hybridization Solution (both components of the Agilent miRNA Complete Labeling and Hyb Kit, P/N 5190-0456). Prior to array hybridization, hybridization mixtures were denatured at 100ºC for 5 minutes and then immediately snap-cooled in ice water for an additional 5 minutes. The samples were hybridized to the Agilent miRNA Microarrays. Hybridization was carried out at 20 RPM at a temperature of 55ºC for 20 hours.

scan_protocol: Scanning and image analysis were performed using the Agilent Feature Extraction (v10.7) software according to the manufacture's guideline.

data_processing:
The data were normalized and analysed using Agilent Feature Extraction software according to the manufacture's guideline.
Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.The normalized value of 90 percentile is further log2 lowess-normalized.
Differentially expressed miRNAs were identified when the probe signal values were larger than 1.0 and the logarithmic miRNA expression ratios were more than 2-fold.

source_name: primary glioblastoma

label_protocol: 200 ng of total RNA was labeled using the Agilent miRNA Complete Labeling and Hyb Kit (P/N 5190-0456). The samples were labeled according to the procedure outlined in the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit Protocol manual (Version 2.0 P/N G4170-90011).

extract_protocol: The formalin-fixed, paraffin-embedded (FFPE) samples from a patient with glioblastoma were made into 5-7 um sections containing tumor areas or adjacent normal tissue areas, which were identified by a neuro-pathologist according to WHO classification of central nervous system tumors (2007). miRNAs were isolated using miRNeasy FFPE Kit (Qiagen) according to the manufacture's protocol.

value: glioblastoma patient

value: female

value: 56 years

tag: tumor who grade

value: IV

tag: tissue type

value: tumor


title: normal tissue

description:
GBM-N
Agilent's microRNA Spike- In kit consists of two microRNA Spike-In solutions for process control.

source_name: adjacent tissue

value: adjacent normal tissue


title: Parent strain_rep1


title: Tumor PX081TT1

status: Public on Sep 16 2014

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

institute: National University of Singapore

description: Laser capture microdissection sample

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: Data were normalized by Robust Multichip Average (RMA) using R with Bioconductor.

source_name: Mammary Gland Cell

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

extract_protocol: Total RNA was extracted by Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Mammary grand cells were isolated from frozen tissue sections using laser capture microdissection.

tag: tumor/nontumor

value: Tumor

value: Mammary Gland Cell from Tumor

tag: scan date (yymmdd)


title: Cefoperazone (CPZ) resistant strain_Line1

source_name: Exponential culture of CPZ resistant strain Line1

value: Cefoperazone (CPZ) resistant strain Line1


title: Tumor PX077TT1

description: Laser capture microdissection sample


title: Tumor PX076TT1

description: Laser capture microdissection sample


title: Tumor PX080TT1

description: Laser capture microdissection sample


title: Tumor PX072TT1

description: Laser capture microdissection sample


title: Tumor PX063TT1

description: Laser capture microdissection sample


title: Tumor PX071TT1

description: Laser capture microdissection sample


title: Tumor PX061TT1

description: Laser capture microdissection sample


title: Tumor PX069TT1

description: Laser capture microdissection sample


title: Tumor PX062TT1

description: Laser capture microdissection sample


title: A549-8 weeks-0-rep 2

description: Sample name: 522828

hyb_protocol: The pellet was dissolved in hybridization solution using the NimbleGen Hybridization kit. After denaturing the probe was hybridized overnight on the 2.1M Deluxe Promoter Arrays using the HX1 mixers and the NimbleGen Hybridization system 4.

scan_protocol: Slides were scanned using the 2 µm high resolution NimbleGen MS 200 micro array scanner per manufacturer's protocol.

data_processing:
Signal intensity data was extracted from the scanned images of each array using NimbleScan v2.6 software and quantile normalized on a per channel basis. Log2 ratios of the intensities were computed (ratio of MeDIP signal/Input signal) for each array. Detection of differential methylation was performed using the Probe Sliding Window-ANOVA algorithm (PSW-ANOVA). PSW-ANOVA (Roche NimbleGen) leverages the “neighbor effect” characteristics of Methylation Dependent ImmunoPrecipitation on chip (MeDIP-chip) data from high density oligonucleotide arrays, where enriched fragments sizes far exceed the spacing between probes. In other words, probes within close proximity have a greater likelihood of reporting signals derived from the same enriched fragment during MeDIP procedure. PSW-ANOVA uses a sliding window approach to identify potential sites of differential enrichment and then assigns probability scores (p values) to each probe on the array using a repeated measure ANOVA model. PSW-ANOVA is implemented in the R statistical programming environment as a custom script and was provided by Roche NimbleGen in collaboration.
Briefly, for each probe, a sliding window is determined based on the sliding window size parameter, centering on the probe in question. Within each sliding window, a repeated measures ANOVA is used to assess the difference between the various experimental groups for all probes located within the sliding window, using the probe ID as the reference to reduce the amount of error arising from different probes within a sliding window. It is assumed that the background and non-specific hybridization behavior of adjacent probes within a sliding window can be larger than the changes in intensity difference between the two channels, but within the sliding window, the log ratios will still be proportional to the intensity difference between groups of samples.
PSW-ANOVA (sliding window of 750 bp comprising 7 probes, and a FDR adjusted p- value < 0.05) was used to identify differential methylated regions (DMR) which were statistically significantly different between the different conditions tested in the experiment. Peaks were identified in the DMR by searching for the number of probes (default = 2) above a p-value minimum cutoff (-log10, default = 1.3) within 150 bp distance of each other. Peaks within 500 bp were merged. Peaks were mapped to promoter regions (from 3 kb upstream to 1 kb downstream of the transcription start site) and CpG islands of genes using the NimbleScan v2.6 software.

source_name: Input DNA from A549 cells exposed to zero dose of sodium arsenite for 8 weeks replicate 2

label_protocol:
Genomic DNAs were sonicated to obtain fragments ranging from 200 bp to 1000 bp, cleaned up using silica columns (Zymo Research) and eluted in TE buffer. 4.4 µg of each sonicated sample was dissolved in a total volume of 495 µL TE buffer. Ten percent of such prepared mixtures was kept as Input sample (Input) at 4°C, while the remaining was immunoprecipitated with 12 µL of a monoclonal antibody against 5’-methylcytidine (Eurogentec) as described by Weber et al (Weber M, JJ Davies, D Wittig, EJ Oakeley, M Haase, WL Lam and D Schubeler. 2005. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37: 853-862.). Immunoprecipitated DNAs (MeDIP) were purified using silica columns (Zymo Research) and eluted in TE buffer. Forty ng of both Input and MeDIP samples were whole genome amplified (WGA) using the WGA2 kit (Sigma Aldrich) following the manufacturer’s instruction, but omitting the fragmentation step. WGA reactions were cleaned up using silica columns (Sigma Aldrich) and eluted in water.
Labeling and hybridization of arrays was performed according to the manufactures’ protocol. In brief, 1 µg of Input DNA and 1 µg of MeDIP DNA were labeled with Cy3 and Cy5 respectively by random priming using the Dual Color DNA labeling kit (Roche NimbleGen). The labeled samples were precipitated using isopropanol and quantified spectrophotometrically using the NanoDrop 1000.

extract_protocol: Cells were washed twice with Hank's Buffered Salt Solution (Invitrogen) and trypsinized. Cell pellets were resuspended in 500 µl digestion buffer (1 mM EDTA; 50 mM Tris–HCl, pH 8.0; 5% SDS) and proteinase K (1 mg/ml) (Ambion) was added. After incubation of 1 hour at 55 °C, the proteinase K was inactivated at 80 °C. RNAse A (400 µg/ml) (Qiagen) treatment was performed for 1 hour at 37 °C. An equal amount of phenol-chloroform-isoamylalcohol (PCI; 25:24:1) (Sigma) was added and shaked manually for 5 min. After centrifugation, the upper phase was again treated with PCI until no protein was visible at the interphase. The upper phase was precipitated with 50 µl 3M NaAc pH 5.6 and 1250 µl cold 100% ethanol. The DNA pellet was washed with cold 70% ETOH, dissolved in 50µl nuclease free water and quantified spectrophotometrically using the NanoDrop 1000 (Thermo Scientific, Waltham, MA). The total amount was at least 10 µg DNA, the 260/280 ratio laid between 1.7-1.9, and the 260/230 was higher than 1.6.

value: A549 human epithelial lung carcinoma cells

value: zero dose of sodium arsenite

value: 8 weeks

tag: sample type

value: input DNA

source_name: medip DNA from A549 cells exposed to zero dose of sodium arsenite for 8 weeks replicate 2

tag: antibody

value: monoclonal antibody against 5’-methylcytidine (Eurogentec, Weber et al (2005), PMID:16007088)

value: immunoprecipitated methyl-DNA (MeDIP)


title: Tumor PX056TT1

description: Laser capture microdissection sample


title: Tumor PX059TT1

description: Laser capture microdissection sample


title: Tumor PX053TT1

description: Laser capture microdissection sample


title: Tumor PX052TT1

description: Laser capture microdissection sample


title: A549-8 weeks-0.08-rep 2

description: Sample name: 522516

source_name: Input DNA from A549 cells exposed to 0.08 µM of sodium arsenite for 8 weeks replicate 2

value: 0.08 µM of sodium arsenite

source_name: medip DNA from A549 cells exposed to 0.08 µM of sodium arsenite for 8 weeks replicate 2


title: A549-8 weeks-0.4-rep 2

description: Sample name: 522505

source_name: Input DNA from A549 cells exposed to 0.4 µM of sodium arsenite for 8 weeks replicate 2

value: 0.4 µM of sodium arsenite

source_name: medip DNA from A549 cells exposed to 0.4 µM of sodium arsenite for 8 weeks replicate 2


title: A549-2 weeks-0.08-rep 2

description: Sample name: 522746

source_name: Input DNA from A549 cells exposed to 0.08 µM of sodium arsenite for 2 weeks replicate 2

value: 2 weeks

source_name: medip DNA from A549 cells exposed to 0.08 µM of sodium arsenite for 2 weeks replicate 2


title: Tumor PX060TT1

description: Laser capture microdissection sample


title: Tumor PX047TT1

description: Laser capture microdissection sample


title: Tumor PX048TT1

description: Laser capture microdissection sample


title: Tumor PX050TT1

description: Laser capture microdissection sample


title: Tumor PX049TT1

description: Laser capture microdissection sample


title: Tumor PX051TT1

description: Laser capture microdissection sample


title: A549-8 weeks-2-rep 1

description: Sample name: 522512

source_name: Input DNA from A549 cells exposed to 2 µM of sodium arsenite for 8 weeks replicate 1

value: 2 µM of sodium arsenite

source_name: medip DNA from A549 cells exposed to 2 µM of sodium arsenite for 8 weeks replicate 1


title: A549-1 week-0.08-rep 2

description: Sample name: 522508

source_name: Input DNA from A549 cells exposed to 0.08 µM of sodium arsenite for 1 week replicate 2

value: 1 week

source_name: medip DNA from A549 cells exposed to 0.08 µM of sodium arsenite for 1 week replicate 2


title: A549-8 weeks-0.4-rep 1

description: Sample name: 522507

source_name: Input DNA from A549 cells exposed to 0.4 µM of sodium arsenite for 8 weeks replicate 1

source_name: medip DNA from A549 cells exposed to 0.4 µM of sodium arsenite for 8 weeks replicate 1


title: A549-2 weeks-2-rep 2

description: Sample name: 471226

source_name: Input DNA from A549 cells exposed to 2 µM of sodium arsenite for 2 weeks replicate 2

source_name: medip DNA from A549 cells exposed to 2 µM of sodium arsenite for 2 weeks replicate 2


title: A549-2 weeks-0.4-rep 2

description: Sample name: 471215

source_name: Input DNA from A549 cells exposed to 0.4 µM of sodium arsenite for 2 weeks replicate 2

source_name: medip DNA from A549 cells exposed to 0.4 µM of sodium arsenite for 2 weeks replicate 2


title: A549-1 week-0.4-rep 2

description: Sample name: 522509

source_name: Input DNA from A549 cells exposed to 0.4 µM of sodium arsenite for 1 week replicate 2

source_name: medip DNA from A549 cells exposed to 0.4 µM of sodium arsenite for 1 week replicate 2


title: A549-1 week-2-rep 2

description: Sample name: 522551

source_name: Input DNA from A549 cells exposed to 2 µM of sodium arsenite for 1 week replicate 2

source_name: medip DNA from A549 cells exposed to 2 µM of sodium arsenite for 1 week replicate 2


title: Tumor PX042TT1

description: Laser capture microdissection sample

source_name: Mammary Gland Cell


title: Tumor PX029TT1

description: Laser capture microdissection sample


title: A549-8 weeks-2-rep 2

description: Sample name: 522832

source_name: Input DNA from A549 cells exposed to 2 µM of sodium arsenite for 8 weeks replicate 2

source_name: medip DNA from A549 cells exposed to 2 µM of sodium arsenite for 8 weeks replicate 2


title: A549-8 weeks-0-rep 1

description: Sample name: 522506

source_name: Input DNA from A549 cells exposed to zero dose of sodium arsenite for 8 weeks replicate 1

source_name: medip DNA from A549 cells exposed to zero dose of sodium arsenite for 8 weeks replicate 1


title: A549-2 weeks-0-rep 2

description: Sample name: 522552

source_name: Input DNA from A549 cells exposed to zero dose of sodium arsenite for 2 weeks replicate 2

source_name: medip DNA from A549 cells exposed to zero dose of sodium arsenite for 2 weeks replicate 2


title: Tumor PX028TT1

description: Laser capture microdissection sample


title: Tumor PX019TT1

description: Laser capture microdissection sample


title: Tumor PX037TT1

description: Laser capture microdissection sample


title: Tumor PX032TT1

description: Laser capture microdissection sample


title: A549-1 week-0-rep 2

description: Sample name: 522518

source_name: Input DNA from A549 cells exposed to zero dose of sodium arsenite for 1 week replicate 2

source_name: medip DNA from A549 cells exposed to zero dose of sodium arsenite for 1 week replicate 2


title: Tumor PX025TT1

description: Laser capture microdissection sample


title: A549-1 week-0.08-rep 1

description: Sample name: 522532

source_name: Input DNA from A549 cells exposed to 0.08 µM of sodium arsenite for 1 week replicate 1

source_name: medip DNA from A549 cells exposed to 0.08 µM of sodium arsenite for 1 week replicate 1


title: Tumor PX022TT1

description: Laser capture microdissection sample


title: Tumor PX008TT1

description: Laser capture microdissection sample


title: Tumor PX009TT1

description: Laser capture microdissection sample


title: Tumor PX006TT1

description: Laser capture microdissection sample


title: Tumor PX039TT1

description: Laser capture microdissection sample


title: Tumor PX012TT1

description: Laser capture microdissection sample


title: Tumor PX016TT1

description: Laser capture microdissection sample


title: A549-2 weeks-2-rep 1

description: Sample name: 522699

source_name: Input DNA from A549 cells exposed to 2 µM of sodium arsenite for 2 weeks replicate 1

source_name: medip DNA from A549 cells exposed to 2 µM of sodium arsenite for 2 weeks replicate 1


title: Tumor PX010TT1

description: Laser capture microdissection sample


title: A549-2 weeks-0-rep 1

description: Sample name: 522554

source_name: Input DNA from A549 cells exposed to zero dose of sodium arsenite for 2 weeks replicate 1

source_name: medip DNA from A549 cells exposed to zero dose of sodium arsenite for 2 weeks replicate 1


title: A549-8 weeks-0.08-rep 1

description: Sample name: 522504

source_name: Input DNA from A549 cells exposed to 0.08 µM of sodium arsenite for 8 weeks replicate 1

source_name: medip DNA from A549 cells exposed to 0.08 µM of sodium arsenite for 8 weeks replicate 1


title: Tumor PX005TT1

description: Laser capture microdissection sample

source_name: Mammary Gland Cell


title: Tumor PX003TT1

description: Laser capture microdissection sample


title: Tumor PX001TT1

description: Laser capture microdissection sample


title: Tumor PX002TT1

description: Laser capture microdissection sample


title: A549-2 weeks-0.4-rep 1

description: Sample name: 522515

source_name: Input DNA from A549 cells exposed to 0.4 µM of sodium arsenite for 2 weeks replicate 1

source_name: medip DNA from A549 cells exposed to 0.4 µM of sodium arsenite for 2 weeks replicate 1


title: A549-1 week-0-rep 1

description: Sample name: 522519

source_name: Input DNA from A549 cells exposed to zero dose of sodium arsenite for 1 week replicate 1

source_name: medip DNA from A549 cells exposed to zero dose of sodium arsenite for 1 week replicate 1