title: pre_50

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

description: total RNA from blood derived before exposure to swimming pool water, individual 50

hyb_protocol: 1500 ng of cRNA was hybridized to the Illumina HumanHT-12v3 Expression BeadChips (Illumina Inc., San Diego, CA, USA). Chips were incubated over night, and washed according to Illumina protocol (technical note 1226030 Rev. B). Hybridization, washing and staining steps were performed manually following strictly the manufacturer’s standardized procedures described in the “Whole-Genome Gene Expression Direct Hybridization Assay Guide” (Illumina Part # 11286331 Rev. A).

scan_protocol: Fluorescence signal was detected on an Illumina Beadarray scanner using Beadscan software (Illumina Inc., San Diego, CA, USA). After background subtraction, raw intensity data (idat) files were produced using Illumina GenomeStudio software.

data_processing: Both preprocessing and downstream analyses of gene expression data were based on Dunning protocol (Dunning 2014; Dunning et al. 2013, 2007). Preprocessing included quality control of the data, filtering of probes, normalization, batch removal, and transformation. From the initial pool of probes (N=49,895) we removed the 319 unmapped probes and compared the hybridization performance with controls, and conducted a quality control of the array information. We then filtered unknown or mismatched annotation, and corroborated phenotypic sex according to chromosome Y RNA expression. An additional filtering step was performed removing all the potential cross reactivity (15,214 probes excluded) and polymorphism probes reported in literature (Ramasamy et al. 2013). From the remaining, 12 probes had missing values and were removed. Finally, we extended the filtering to Illumina reported polymorphisms or cross reactivity probes removing 8,327 additional probes. In total, 26,023 probes were suited to our analyses and were used in the models. Expression intensities were quantile normalized, and log2 transformed. As the expression analyses were performed in several laboratory batches. We normalized by batch to reduce this technical variation. All the statistical and bioinformatic analyses were performed in R v.3.0.2 using Beadarray and limma packages (Dunning et al. 2007; R Development Core Team 2013; Smyth 2004). We reported the Log-Fold change (LogFC) per gene, and corrected per multiple comparisons using False Discovery Rate (FDR) using the Benjamini-Hochberg correction (Benjamini and Hochberg 1995).

source_name: peripheral blood

label_protocol: 200 ng of RNA was reverse-transcribed into cRNA and biotin-UTP labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

extract_protocol: Blood was collected in PAXgene blood RNA tubes (PreAnalytiX, Switzerland) in order to preserve intracellular RNA integrity and stored at -80ºC. RNA extractions were performed using the PAXgene Blood RNA Kit (Ref. 762174, Qiagen, Germany), in four different batches in 2009. Isolated RNA was quality controlled with an Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA) and quantified in a NanoDrop 1000 UV-Vis Spectrophotometer (ThermoScientific, Wilmington, DE, USA). All the samples had a RNA Integrity Number (RIN) higher than 7.0 (Schroeder et al. 2006), an optical density-OD (A260/A280) ratio value >1.8 and an OD (A260/A230) ratio >1.5. Genome Wide Expression analysis (GWE) was performed on 76 samples in four batches using HumanHT-12 v3 Expression BeadChip Kits.

treatment_protocol: We conducted an experimental crossover design in nonsmoking adult volunteers recruited through open advertisements on the Internet and at local universities in Barcelona, Spain. Volunteers were screened to verify eligibility (nonsmoking adults, 18–50 years of age, without a diagnosis of asthma; without respiratory symptoms in the previous 3 weeks). Participants were asked about sociodemographics, sport practice, water consumption and use, and history of allergies and eczema. Weight and height were measured with standard procedures. Body mass index was calculated as the weight in kilograms over the squared height in meters. Body surface area was calculated using Mosteller formula (Mosteller 1987). Per protocol, all the participants should abstain from visiting swimming pools during the week before the assessment and also to abstain from taking a shower on the day of the experiment. The study was approved by the ethics committee of the research center according to national and international regulations. The volunteers signed an informed consent before participation.   A single indoor 25-m-long chlorinated swimming pool in Barcelona, Spain, was used. Participants were evaluated between 09:00 and 14:00 hours (before lunch) in May, June, September, or October 2007. Volunteers were allowed to swim at their pace and rest whenever they wanted. Blood samples were collected before and after 40 minute swimming to evaluate gene expression according to a strict schedule previously described (Font-Ribera et al. 2010). Biological samples and other measurements were obtained in a room inside the sports center apart from the swimming pool area. From the total sample (50 volunteers), RNA measurements were available for only 33 randomly selected subjects. Four of the individuals (subject numbers 16, 32, 48 and 49) were subjected to the entire procedure twice generating a second independent set of replicate samples, and the samples of one subject were finally excluded from he analysis. This sums up to a total of 74 samples (37 sample pairs, before and after exposure, derived from 33 individuals).

tag: subject

tag: experimental repetition for same subject

tag: swimming pool water exposure time

value: 0 minutes

tag: exhaled bromoform

tag: metabolic equivalents

tag: gender

value: female

tag: age


title: post_50

status: Public on Sep 07 2015

type: RNA

city: Badalona

country: Spain

institute: IGTP

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 50

molecule: total RNA

organism: Homo sapiens

value: 40 minutes


title: 49366-Normal-Diaphragm

city: Chapel Hill

first: Richard

last: Moffitt

state: NC

address: 450 West Drive

country: USA

institute: University of North Carolina

hyb_protocol: As described in Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp labeling) v 5.7 [Manual G4140-90050]

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent G2505C fluorescent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction (v10.5) software.

data_processing: log2 Cy5 signal was analyzed after setting negative values to zero. Probe data were collapsed by gene symbol via mean expression. Samples were quantile normalized to the subset of genes with less than 0.5 standard deviation across primary, metastatic, and normal samples. Data were processed in MATLAB R2013a.

source_name: Human Reference

extract_protocol: Qiagen Rneasy Kit

tag: sample type

value: Stratagene Human reference RNA

tag: cell line/tissue

value: Diaphragm

tag: tissue type

value: Normal


title: post_48.2

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 48, replicate 2


title: post_45

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 45


title: 48590-Normal-Liver

label_protocol: As described in Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp labeling) v 5.7 [Manual G4140-90050]

value: Liver


title: 49369-Normal-Pancreas

value: Pancreas


title: pre_46

description: total RNA from blood derived before exposure to swimming pool water, individual 46


title: pre_44

description: total RNA from blood derived before exposure to swimming pool water, individual 44


title: post_47

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 47


title: post_46

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 46


title: 48593-Normal-Lung

value: Lung


title: pre_49.2

description: total RNA from blood derived before exposure to swimming pool water, individual 49, replicate 2

value: male


title: pre_48.2

description: total RNA from blood derived before exposure to swimming pool water, individual 48, replicate 2


title: post_44

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 44


title: pre_43

description: total RNA from blood derived before exposure to swimming pool water, individual 43


title: 48595-Normal-Spleen

value: Spleen


title: pre_45

description: total RNA from blood derived before exposure to swimming pool water, individual 45


title: 49372-Normal-Liver


title: pre_47

description: total RNA from blood derived before exposure to swimming pool water, individual 47


title: 49373-Normal-Liver


title: 48580-Normal-Diaphragm


title: post_43

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 43


title: 48585-Normal-Lung


title: post_49.2

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 49, replicate 2


title: pre_42

description: total RNA from blood derived before exposure to swimming pool water, individual 42


title: 48575-Normal-Diaphragm


title: 48579-Normal-Pancreas


title: post_41

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 41


title: post_42

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 42


title: 49361-Normal-Vessel

value: Vessel


title: 48576-Normal-Pancreas


title: 49371-Normal-Liver


title: pre_40

description: total RNA from blood derived before exposure to swimming pool water, individual 40


title: post_40

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 40


title: 48588-Normal-Spleen


title: 48583-Normal-Liver


title: 48582-Normal-Liver


title: pre_41

description: total RNA from blood derived before exposure to swimming pool water, individual 41


title: post_38

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 38


title: 49358-Normal-LymphNode

value: LymphNode


title: post_39

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 39


title: 48611-Normal-Pancreas


title: pre_38

description: total RNA from blood derived before exposure to swimming pool water, individual 38


title: 48571-Normal-Liver


title: pre_39

description: total RNA from blood derived before exposure to swimming pool water, individual 39


title: 48570-Normal-Liver


title: pre_32.2

description: total RNA from blood derived before exposure to swimming pool water, individual 32, replicate 2


title: post_37

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 37


title: post_32.2

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 32, replicate 2


title: pre_37

description: total RNA from blood derived before exposure to swimming pool water, individual 37


title: 48612-Normal-Fat

value: Fat


title: 48572-Normal-Spleen


title: 48610-Normal-Lung


title: 48573-Normal-LymphNode


title: pre_30

description: total RNA from blood derived before exposure to swimming pool water, individual 30


title: most susceptible, postdose biological rep3

city: Hangzhou

first: Xiaoyan

last: Lu

state: Zhejiang

address: Yuhangtang Road 866

country: China

institute: Zhejiang University

description: gene expression data from the blood sample of one of the 5 most susceptible rats after acetaminophen treatment

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

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

data_processing: Gene expression data from the Affymetrix Rat Genome 230 2.0 chips were loaded into ArrayTrack® (http://www.fda.gov/ScienceResearch/BioinformaticsTools/ArrayTrack). Raw microarray intensity data were normalized per chip to the same median intensity value of 1000.

label: biotin

organism: Rattus norvegicus

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

growth_protocol: The predose and postdose blood samples were collected via retro-orbital plexus from anesthetized animals into a vacutainer-EDTA tube for RNA isolation.

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

treatment_protocol: The red cells in blood samples were lysed within 24 h after samples collection.

tag: hepatotoxicity status

value: susceptible

tag: tissue

value: blood

value: Male

tag: strain

value: Wistar


title: most susceptible, postdose biological rep4

source_name: blood sample of one of the 5 most susceptible rats after acetaminophen treatment


title: most susceptible, postdose biological rep2


title: pre_27

description: total RNA from blood derived before exposure to swimming pool water, individual 27

value: 0 minutes


title: 48609-Normal-Spleen


title: pre_29

description: total RNA from blood derived before exposure to swimming pool water, individual 29

value: female


title: 48605-Normal-Liver

value: Stratagene Human reference RNA


title: post_30

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 30

value: 40 minutes


title: 48607-Normal-Lung

value: Normal


title: most susceptible, postdose biological rep5


title: most susceptible, postdose biological rep1


title: most resistant, postdose biological rep4

description: gene expression data from the blood sample of one of the 5 most resistant rats after acetaminophen treatment

value: resistant


title: post_29

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 29


title: most resistant, postdose biological rep1

source_name: blood sample of one of the 5 most resistant rats after acetaminophen treatment


title: post_26

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 26


title: most resistant, postdose biological rep3


title: post_27

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 27


title: 48608-Normal-Pancreas

value: Pancreas


title: post_24

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 24


title: 49397-Normal-Liver

value: Liver


title: pre_26

description: total RNA from blood derived before exposure to swimming pool water, individual 26

value: male


title: most resistant, postdose biological rep2


title: 48606-Normal-LymphNode


title: 53860-Normal-Spleen

value: Spleen


title: 49395-Normal-Lung

value: Lung


title: most susceptible, predose biological rep2

description: gene expression data from the blood sample of one of the 5 most susceptible rats before acetaminophen treatment


title: pre_24

description: total RNA from blood derived before exposure to swimming pool water, individual 24


title: 49393-Normal-Lung


title: post_23

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 23


title: post_22

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 22


title: pre_23

description: total RNA from blood derived before exposure to swimming pool water, individual 23


title: 53855-Normal-Liver


title: most susceptible, predose biological rep1

source_name: blood sample of one of the 5 most susceptible rats before acetaminophen treatment


title: pre_22

description: total RNA from blood derived before exposure to swimming pool water, individual 22


title: most resistant, predose biological rep4

description: gene expression data from the blood sample of one of the 5 most resistant rats before acetaminophen treatment


title: most susceptible, predose biological rep4


title: 53856-Normal-Pancreas


title: pre_16.2

description: total RNA from blood derived before exposure to swimming pool water, individual 16, replicate 2


title: pre_17

description: total RNA from blood derived before exposure to swimming pool water, individual 17


title: most resistant, predose biological rep5

source_name: blood sample of one of the 5 most resistant rats before acetaminophen treatment


title: 49346-Normal-Spleen


title: 53857-Normal-PelvicWall

value: PelvicWall


title: most resistant, predose biological rep2


title: post_17

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 17


title: 49340-Normal-Liver


title: post_16.2

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 16, replicate 2


title: most resistant, predose biological rep1


title: 53834-Normal-Lung


title: most resistant, predose biological rep3


title: Donor 12_IFNb_WT

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2-transformed and normalized using quantile normalization with Partek Genomics Suite

organism: Mus musculus

source_name: Bone-marrow derived macrophages (BMDM)

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

growth_protocol: Bone marrow-derived macrophages (BMDMs) were obtained by culturing the bone marrow cells of 6- to 8-week old wild type or Atf3–/– C57BL/6 mice in DMEM supplemented with 10% fetal bovine serum, 10 μg/ml ciprofloxacin and 40 ng/ml recombinant human M-CSF (R&D Systems) or 20% L929 conditioned medium. Six days later, BMDMs were collected and plated for experiments. For comparative experiments with Atf3–/– BMDMs age- and sex-matched wild type BMDMs were used.

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

treatment_protocol: Recombinant murine IFNβ was purchased from R&D systems. BMDMs were treated with 1000 U/ml IFNβ for 10h.

tag: mouse model

value: Wild type (WT)

tag: activation stimuli

value: IFNbeta (IFNb)

tag: donor

tag: cell type

value: Bone-marrow derived macrophages


title: post_6

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 6

tag: subject


title: 53851-Normal-Peritoneal

value: Peritoneal


title: post_7

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 7

tag: experimental repetition for same subject


title: Donor 11_untreated_ATF3KO

value: ATF3-deficiency (ATF3KO)

value: untreated


title: most susceptible, predose biological rep3

value: susceptible

value: blood

value: Male

value: Wistar


title: pre_7

description: total RNA from blood derived before exposure to swimming pool water, individual 7

tag: swimming pool water exposure time

value: 0 minutes


title: Donor 10_IFNb_WT


title: 53849-Normal-Diaphragm

value: Stratagene Human reference RNA

value: Diaphragm

value: Normal


title: 49091-Normal-Peritoneal


title: post_5

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 5

value: 40 minutes

tag: exhaled bromoform

value: female


title: 49087-Normal-Lung

value: Lung


title: 53850-Normal-LymphNode

value: LymphNode


title: 49092-Normal-Pancreas

value: Pancreas


title: pre_6

description: total RNA from blood derived before exposure to swimming pool water, individual 6

tag: metabolic equivalents


title: pre_5

description: total RNA from blood derived before exposure to swimming pool water, individual 5

tag: gender


title: post_3

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 3

tag: age


title: 49090-Normal-Lung

tag: sample type


title: pre_3

description: total RNA from blood derived before exposure to swimming pool water, individual 3


title: Donor 9_IFNb_ATF3KO

value: IFNbeta (IFNb)

value: Bone-marrow derived macrophages


title: 49093-Normal-Spleen

tag: cell line/tissue

value: Spleen


title: Donor 5_untreated_ATF3KO

value: ATF3-deficiency (ATF3KO)

value: untreated


title: Donor 6_untreated_WT

value: Wild type (WT)


title: post_4

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 4


title: Donor 8_IFNb_ATF3KO


title: Donor 7_IFNb_WT


title: pre_4

description: total RNA from blood derived before exposure to swimming pool water, individual 4


title: Donor 3_untreated_WT


title: 49089-Normal-Lung

tag: tissue type


title: 49088-Normal-Liver

value: Liver


title: post_57

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 57

value: male


title: post_49.1

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 49, replicate 1


title: pre_49.1

description: total RNA from blood derived before exposure to swimming pool water, individual 49, replicate 1

value: 0 minutes


title: pre_57

description: total RNA from blood derived before exposure to swimming pool water, individual 57


title: Donor 1_untreated_WT


title: Donor 4_IFNb_ATF3KO


title: 49077-Normal-Liver

value: Stratagene Human reference RNA


title: 49078-Normal-Liver


title: 49079-Normal-Fat

value: Fat


title: 49080-Normal-Fat

value: Normal


title: 53840-Normal-Lung


title: 53839-Normal-Liver


title: 49082-Normal-Pancreas


title: 49081-Normal-LymphNode


title: pre_16.1

description: total RNA from blood derived before exposure to swimming pool water, individual 16, replicate 1


title: 53859-Normal-Lung


title: 49074-Normal-Liver


title: most resistant, postdose biological rep5

description: gene expression data from the blood sample of one of the 5 most resistant rats after acetaminophen treatment

tag: hepatotoxicity status

value: resistant

value: blood

value: Male

value: Wistar


title: pre_48.1

description: total RNA from blood derived before exposure to swimming pool water, individual 48, replicate 1

value: female


title: post_48.1

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 48, replicate 1

value: 40 minutes


title: most susceptible, predose biological rep5

description: gene expression data from the blood sample of one of the 5 most susceptible rats before acetaminophen treatment

value: susceptible

tag: tissue


title: 56321-Met-Peritoneal

value: Peritoneal

value: Metastasis


title: 54024-MiaPaca2-CellLine

source_name: CellLine


title: post_10

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 10


title: 56319-Met-Peritoneal


title: WT control, 4

city: Bronx

first: Britta

last: Will

state: NY

address: 1300 Morris Park Avenue

department: Cell Biology

institute: Albert Einstein College of Medicine

hyb_protocol: Following fragmentation, ~5 microg of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Gene 1.0 ST microarray (Affymetrix). GeneChips were washed and stained in an Affymetrix Fluidics Station

scan_protocol: GeneChip® Scanner 3000 7G system (Affymetrix) according to standard protocols.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings; CEL files were generated. CEL files processed/normalized using RMA from the oligo (oligo_1.30.0) Bioconductor package. Values are log2-transformed expression values after RMA-normalization.

source_name: Sorted Lin-cKit+ cells from bone marrow

label_protocol: Biotinylated cRNA were prepared using the GeneChip® WT terminal labeling kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: uncultured primary cells

extract_protocol: Total mRNA was extracted using Qiagen's RNAesy Micro kit according to the manufacturer's instructions; After checking the quality of RNA with an Agilent 2100 Bioanalyzer, total RNA was amplified utilizing Single Primer Isothermal Amplification (SPIA®Nugen Ovation pico WTA) system according to the manufacturer’s instructions.

treatment_protocol: no treatment

tag: genotype/variation

value: wildtype

tag: background strain

value: mixed (R1 embryonic stem cell-derived, Agouti, C57Bl/6)


title: URE-Msh2 AML, 3

source_name: Sorted Lin-cKit+ cells from the bone marrow of a moribund mouse


title: complementation strain, biological replicate 3

status: Public on Sep 06 2015

city: Columbus

first: Binjie

last: Xu

state: OH

address: 460 W. 12th Ave

department: Microbiology

institute: The Ohio State University

hyb_protocol: Samples were hybridized using Herring sperm DNA, acetylated BSA (50mg*ml-1), and hybridization controls (Affymetrix). Samples were heated at 65°C for 5 minutes, 99°C for 5 minutes,and 50°C for 5 minutes. Afterwards, they were centrifuged at top speed for 5 minutes. Then samples were hybridized for 16 hours at 50°C at 60rpm. Fluidics washing was performed via Flex_Midi_Euk2v3.

scan_protocol: samples were scanned with a GeneChip Scanner 3000 7G using AGCC.

data_processing: Data were analyzed via affy and limma packages in Bioconductor.

organism: Pseudomonas aeruginosa

source_name: WFPA510 (complementation strain)

label_protocol: cDNA was synthesized from 10µg total RNA, samples were then enzymatically fragmented with DNase I and the 3’ ends of the fragmentation products were biotinylated with GeneChip DNA Labeling Reagent (Affymetrix, P/N 900542) according to manufacture protocols.

growth_protocol: A single colony of each bacterial strain was resuspended in 400 µl LBNS, and 2 µl were spotted in the middle of the cellophane sheet. After air-drying, plates were incubated un-invertedly in a humid chamber at room temperature for 48 h.

extract_protocol: Total RNA was extracted by the Qiagen RNeasy RNA isolation kit according to manufacture protocols.

treatment_protocol: Bacteria were scraped off from the edge portions of the colonies by sterile P200 tips, and resuspended in fresh LBNS.

tag: strain

tag: amrz functional status


title: post_32.1

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 32, replicate 1


title: URE-Msh2 preleukemic, 1

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings; CEL files were generated. CEL files were processed/normalized using RMA from the oligo (oligo_1.30.0) Bioconductor package. Values are log2-transformed expression values after RMA-normalization.

source_name: Sorted Lin-cKit+ cells from the bone marrow of a preleukemic mouse


title: WT control, 3


title: AmrZV20A strain, biological replicate 2

source_name: WFPA513 (AmrZV20A)

value: Defective


title: post_2

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 2


title: complementation strain, biological replicate 2


title: post_16.1

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 16, replicate 1

value: male


title: WT control, 1

source_name: Sorted Lin-cKit+ cells from bone marrow (pool of 3 animals)


title: pre_10

description: total RNA from blood derived before exposure to swimming pool water, individual 10

value: 0 minutes


title: Donor 2_untreated_ATF3KO

tag: mouse model

value: ATF3-deficiency (ATF3KO)

tag: activation stimuli

value: untreated

tag: donor

tag: cell type

value: Bone-marrow derived macrophages


title: post_1

description: total RNA from blood derived after 40 minutes exposure to swimming pool water, individual 1

tag: subject

tag: experimental repetition for same subject

tag: swimming pool water exposure time

tag: exhaled bromoform


title: ΔamrZ strain, biological replicate 3

source_name: WFPA205 (ΔamrZ)


title: AmrZV20A strain, biological replicate 1


title: URE-Msh2 AML, 2


title: complementation strain, biological replicate 1

value: Normal


title: pre_1

description: total RNA from blood derived before exposure to swimming pool water, individual 1

tag: metabolic equivalents

tag: gender

tag: age


title: ΔamrZ strain, biological replicate 2


title: WT control, 2


title: URE-Msh2 preleukemic, 2


title: pre_32.1

description: total RNA from blood derived before exposure to swimming pool water, individual 32, replicate 1


title: AmrZV20A strain, biological replicate 3


title: genomic DNA from H4 cells

type: genomic

city: Seoul

first: Hye Youn

last: Sung

address: 911-1 Mok-dong

department: Biochemistry

country: South Korea

institute: Ewha Womens University

description: wild type

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: Illumina Genome Studio v2009.2

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

growth_protocol: Human glioblastoma H4 and H4-sw cells were grown in DMEM  containing 10% fetal bovine serum, 100 Units/mL, 100 μg/mL  and 2 mM L-glutamine. For maintaining H4-sw cells, 500 μg/mL geneticine  was additionally supplemented in growth media.

extract_protocol: Genomic DNA was extracted and purified from the cells using Qiagen QIAamp DNA Mini kit according to standard instructions

tag: cell line

tag: origin

value: brain, neuroglioma


title: URE-Msh2 AML, 1

tag: genotype/variation


title: WT P. aeruginosa, biological replicate 3

source_name: PAO1, WT strain


title: WT P. aeruginosa, biological replicate 1


title: genomic DNA from H4-sw cells

description: Swedish double mutation (APP695, K595N/M596L)


title: ΔamrZ strain, biological replicate 1


title: pre_2

description: total RNA from blood derived before exposure to swimming pool water, individual 2


title: Mouse Liver_Mammea_biological rep1

city: Mexico City

first: Juan

middle: Carlos

last: Gomez-Verjan

state: Distrito Federal

address: Circuito Exterior, Ciudad Universitaria, Delegación Coyoacán C.P. 04510, México, D.F.

department: Productos Naturales

country: Mexico

institute: Instituto de Quimica

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were primary processed using arrayQuialityMetrics package to asses quality of raw data. Raw data were summarized from the corrected intensities and then quantile normalized using RMA method. Finally differential expressed genes obtained with Ingenuity Software

source_name: liver, mammea A/BA+A/BB

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: The mice were housed individually in cages and maintained (23 ± 2 °C and 40%–60% humidity) under a standard 12-h light/dark cycle with free access to purified water and commercial diet. The mice were habituated for 7 days before the experiment. All experimental procedures were approved by the Ethics Committee

extract_protocol: Liver of animals was immediately obtained after sacrifice and samples immediately homogenized with PureLink RNA Mini Kit. Integrity of RNA was determinated by using a Bioanalyzer

treatment_protocol: Soulatrolide, Mammea A/BA+A/BB (3:1) for a whole week at a dose of 20mg/Kg/daily orally given

value: Male

tag: tissue

value: liver

tag: treatment

value: Mammea A/BA+A/BB (3:1)


title: WT P. aeruginosa, biological replicate 2

tag: strain

tag: amrz functional status


title: Mouse Liver_Soulatrolide_biological rep2

source_name: liver, soulatrolide

value: Soulatrolide


title: Mouse Liver_Soulatrolide_biological rep3


title: Mouse Liver_Mammea_biological rep2


title: Mouse Liver_Soulatrolide_biological rep1


title: Mouse Liver_Control_biological rep4

source_name: liver, control (SSI)

value: Control


title: Mouse Liver_Control_biological rep3


title: RA 212 Memory T effector

status: Public on Sep 05 2015

city: Måløv

first: Klaus Stensgaard

last: Frederiksen

address: Novo Nordisk Park F9.1.07

department: Molecular Genetics

country: Denmark

institute: Novo Nordisk A/S

description: Gene expression profiling of purified Memory T effectors from RA patient

hyb_protocol: Affymetrix EukGE-WS2v5

scan_protocol: Affymetrix cel analysis

data_processing: Bioconductor/R RMA

source_name: Memory T effectors from RA patient

label_protocol: Affymetrix in vitro transcription

extract_protocol: Total RNA was isolated using the standard TRIzol protocol (Invitrogen, Carlsbad, CA), but with subsequent RNA clean-up of the water phase using the RNeasy Qiagen MinElute kit (Qiagen, Germantown, MD). The quality of the RNA was confirmed on the Agilent Bioanalyzer using RNA Nano chips (Agilent Technologies, Santa Clara, CA).

value: purified Memory T effectors

tag: disease state

value: rheumatoid arthritis


title: RA 212 Memory Treg

description: Gene expression profiling of purified Memory Tregs from RA patient

source_name: Memory Tregs from RA patient

tag: donor

value: purified Memory Tregs


title: RA 212 Naive T effector

description: Gene expression profiling of purified Naive T effectors from RA patient

source_name: Naive T effectors from RA patient

tag: cell type

value: purified Naive T effectors


title: Mouse Liver_Mammea_biological rep3


title: Mouse Liver_Control_biological rep1


title: RA 211 Memory T effector


title: Mouse Liver_Control_biological rep2


title: RA 211 Naive T effector


title: RA 211 Memory Treg


title: RA 211 Naive Treg

description: Gene expression profiling of purified Naive Tregs from RA patient

source_name: Naive Tregs from RA patient

value: purified Naive Tregs


title: RA 212 Naive Treg


title: RA 209 Memory T effector


title: RA 209 Memory Treg


title: RA 209 Naive T effector


title: RA 208 Naive T effector


title: RA 208 Memory Treg


title: RA 208 Memory T effector


title: RA 208 Naive Treg


title: RA 209 Naive Treg


title: RA 207 Memory Treg


title: RA 207 Memory T effector


title: Peripheral blood Spo45N

city: Mishima

first: Takahide

last: Hayano

state: Shizuoka

address: Yata 1111

department: Division of Human Genetics

country: Japan

institute: National Institute of Genetics

description: Hybridized to Genome-Wide Human SNP Array 6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed, stained, and scanned with a Gene Chip Scanner 3000 7G.

data_processing: CEL files were processed by PennCNV using PennCNV-Affy protocol.

label: Biotin

source_name: Patient with high-grade ovarian cancer Spo45

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was isolated from cancer tissues using a phenol-chloroform method and from peripheral blood using the QIAamp DNA Blood Maxi Kit.

value: high-grade ovarian cancer

tag: individual

value: Peripheral blood

tag: tumor grade


title: High-grade serous ovarian cancer tissue Spo45T

value: Ovary


title: RA 207 Naive T effector


title: RA 207 Naive Treg


title: Peripheral blood Spo44N

source_name: Patient with high-grade ovarian cancer Spo44


title: High-grade serous ovarian cancer tissue Spo41T

source_name: Patient with high-grade ovarian cancer Spo41


title: High-grade serous ovarian cancer tissue Spo46T

source_name: Patient with high-grade ovarian cancer Spo46


title: High-grade serous ovarian cancer tissue Spo49T

source_name: Patient with high-grade ovarian cancer Spo49


title: Peripheral blood Spo41N


title: High-grade serous ovarian cancer tissue Spo40T

source_name: Patient with high-grade ovarian cancer Spo40


title: High-grade serous ovarian cancer tissue Spo44T


title: High-grade serous ovarian cancer tissue Spo39T

source_name: Patient with high-grade ovarian cancer Spo39


title: RA 206 Memory T effector


title: Peripheral blood Spo49N


title: High-grade serous ovarian cancer tissue Spo38T

source_name: Patient with high-grade ovarian cancer Spo38


title: RA 206 Naive Treg


title: Peripheral blood Spo35N

source_name: Patient with high-grade ovarian cancer Spo35


title: High-grade serous ovarian cancer tissue Spo36T

source_name: Patient with high-grade ovarian cancer Spo36


title: RA 206 Memory Treg


title: Peripheral blood Spo46N


title: HC6 Memory T effector

description: Gene expression profiling of purified Memory T effectors from healthy control

source_name: Memory T effectors from healthy control

value: healthy control


title: Peripheral blood Spo38N


title: Peripheral blood Spo40N


title: Peripheral blood Spo39N


title: Peripheral blood Spo33N

source_name: Patient with high-grade ovarian cancer Spo33


title: HC6 Naive T effector

description: Gene expression profiling of purified Naive T effectors from healthy control

source_name: Naive T effectors from healthy control


title: Mir22 KO nCB 2

city: Houston

first: David

middle: Brian

last: Corry

address: One Baylor Plaza

department: Medicine

institute: Baylor College of Medicine

description:
SAMPLE 11
Mir22 deficient mice exposed to nCB, Replicate 2

hyb_protocol: 750 ng of purified biotinylated cRNA was added to Hybridization Cocktail Buffer (Illumina), applied to arrays, and incubated at 58°C for 16 hours.

scan_protocol: Following hybridization, arrays were washed and stained using standard Illumina procedures before scanning on an Illumina iScan instrument using the DirectHyb Tiff setting. Scanned images were processed by the Gene Expression module of GenomeStudio (v 1.6, Illumina) using default parameters without normalization.

data_processing: Detected genes were first filtered according to detection p-values (p<0.05 in at least one sample).  The expression value were QuantileScrunched(QS)-normalized, background-subtracted and LOG2 transformed in GenomeStudio by Expression Analysis Inc.

source_name: Lung CD11c+ cells

label_protocol: RNA samples were converted into labeled target cRNA using the Illumina TotalPrep-96 RNA Amplification Kit (Ambion). Briefly, 100 ng of total RNA was converted to double-stranded cDNA using an oligo-d(T) primer-adaptor. This cDNA was purified using magnetic beads and used as a template for in vitro transcription using T7 RNA Polymerase and biotin-UTP. The resulting biotinylated cRNA was purified using magnetic beads and quantitated by spectrophotometry.

extract_protocol: Total RNA extraction were performed by Expression Analysis Inc. according to their standard protocol. (http://www.q2labsolutions.com/genomics-laboratories/dna-and-rna-services)

treatment_protocol: Two month old wildtype mice and Mir22-/- mice are exposed to nCB for one month.  Lung CD11c+ cells were isolated using AutoMACS.  Isolated cells were snap freezed in liquid nitrogen and sent to Expression Analysis company for the following procession.

value: B6(Cg)-Tyrc-2J/ J

value: 4 month

value: Mir22 KO

tag: stress

value: nCB

value: lung

value: APC


title: High-grade serous ovarian cancer tissue Spo33T


title: High-grade serous ovarian cancer tissue Spo35T


title: High-grade serous ovarian cancer tissue Spo32T

source_name: Patient with high-grade ovarian cancer Spo32


title: High-grade serous ovarian cancer tissue Spo31T

source_name: Patient with high-grade ovarian cancer Spo31


title: Mir22 KO nCB 3

description:
SAMPLE 12
Mir22 deficient mice exposed to nCB, Replicate 3


title: Mir22 KO nCB 1

description:
SAMPLE 10
Mir22 deficient mice exposed to nCB, Replicate 1


title: HC5 Memory T effector


title: HC6 Naive Treg

description: Gene expression profiling of purified Naive Tregs from healthy control

source_name: Naive Tregs from healthy control


title: RA 206 Naive T effector

source_name: Naive T effectors from RA patient


title: WT nCB 2

description:
SAMPLE 8
wild-type mice exposed to nCB, Replicate 2

value: wild-type


title: HC4 Memory T effector


title: HC4 Memory Treg

description: Gene expression profiling of purified Memory Tregs from healthy control

source_name: Memory Tregs from healthy control


title: HC5 Memory Treg


title: Peripheral blood Spo36N


title: WT nCB 1

description:
SAMPLE 7
wild-type mice exposed to nCB,Replicate 1


title: HC5 Naive T effector


title: HC4 Naive T effector


title: Mir22 KO PBS 3

description:
SAMPLE 6
Mir22 deficient mice exposed to PBS, Replicate 3

value: PBS


title: WT nCB 3

description:
SAMPLE 9
wild-type mice exposed to nCB, Replicate 3


title: High-grade serous ovarian cancer tissue Spo25T

source_name: Patient with high-grade ovarian cancer Spo25


title: HC3 Memory T effector

value: purified Memory T effectors


title: HC5 Naive Treg


title: Peripheral blood Spo32N


title: HC4 Naive Treg


title: HC3 Naive Treg


title: Mir22 KO PBS 2

description:
SAMPLE 5
Mir22 deficient mice exposed to PBS,Replicate 2


title: HC3 Naive T effector


title: HC2 Memory Treg


title: HC1 Memory Treg


title: HC3 Memory Treg


title: HC2 Memory T effector


title: Mir22 KO PBS 1

description:
SAMPLE 4
Mir22 deficient mice exposed to PBS, Replicate 1


title: Peripheral blood Spo31N


title: Peripheral blood Spo25N


title: WT PBS 3

description:
SAMPLE 3
wild-type mice exposed to PBS, Replicate 3


title: HC1 Naive T effector


title: HC1 Naive Treg


title: WT PBS 2

description:
SAMPLE 2
wild-type mice exposed to PBS,Replicate 2


title: HC2 Naive T effector


title: HC2 Naive Treg


title: WT PBS 1

description:
SAMPLE 1
wild-type mice exposed to PBS, Replicate 1


title: HC6 Memory Treg


title: HC1 Memory T effector


title: High-grade serous ovarian cancer tissue Spo20T

description: Hybridized to Genome-Wide Human SNP Array 6.0

source_name: Patient with high-grade ovarian cancer Spo20


title: stage 40

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Gene expression at stage 35

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Xenopus laevis Custom GE Microarrays (G2514F 015932) 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 by brief centrifugation.

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

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: 015932_D_20070204).

organism: Xenopus laevis

source_name: stage 40, whole embryo

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Embryos were dejellied and cultured in 10% Steinberg's solution. Embryos were staged according to the Nieuwkoop and Faber staging table.

extract_protocol: Total RNA was prepared using ISOGEN (Nippon Gene) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: developmental stage

value: stage 40

value: whole embryo


title: Hybrid between S. cerevisiae and S. kudriavzevii Lalvin VIN7 replicate B, fermentation at 28ºC

city: Paterna

first: Amparo

last: Gamero

state: Valencia

address: Avda. Agustín Escardino 7

department: Food Biotechnology

institute: IATA-CSIC

description: Gene expression of the hybrid between S. cerevisiae and S. kudriavzevii VIN7 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C. Replicate B

hyb_protocol: A mixture of 200 to 300 pmol of the two samples labelled was concentrated in a Concentrator Plus (Eppendorf™, Hamburg, Germany). Competitive hybridization was performed in hybridization chambers AHC (ArrayIt Corporation, CA, USA) at 42°C overnight.  (Prehybridization solution contained 3X SSC, 0.1% SDS and 0.1 mg/ml BSA; hybridization solution contained 5X SSC, 0.1% SDS and 0.1 mg/ml of salmon DNA. Microarrays were washed manually with different solutions containing different SSC 20X and SDS 10% concentrations (Sol.1: 2X SSC-0.1% SDS; Sol.2: 0.1X SSC-0.1% SDS; Sol.3: 0.1 SSC; Sol4: 0.01X SSC).

scan_protocol: Signal intensities of Cy3 and Cy5 were acquired with an Axon GenePix 4100A scanner (Molecular devices, CA, USA) using GenePix Pro v.6.1 software, at a resolution of 10 μm.

data_processing:
Raw data with a global background subtraction were generated from GenePix pro 6.0. Analyses were done using Acuity 4.0 software (Molecular Devices, CA, USA).The individual data sets were normalized to a log2 ratio value of 1. After normalization, data were filtered to remove spots flagged as not found. Only spots with at least two replicates were considered. Finally, replicates were combined and their medians were calculated.
Genes with a two-fold log2 ratio values were considered to be significantly expressed.

organism: Saccharomyces cerevisiae x Saccharomyces kudriavzevii

source_name: yeast cells from wine fermentation at 28C

label_protocol: 2-4 ug of total RNA was linearly amplified using the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies™, Ca, USA). 2-3 ug of amplified cRNA was used as template for cDNA synthesis. cDNA was marked indirectly with “SuperScript™ Indirect cDNA Labeling System” (Invitrogen™, SanDiego, CA). The fluorophores used were Cy3 and Cy5 mono-reactiveDye (Amersham GE Healthcare™, Amersham UK) and dye incorporation was monitored by a Nanodrop spectrophotometer.

growth_protocol: Wine fermentations in Tempranillo must at 12C or 28C

extract_protocol: RNA extraction method was based on consecutive treatments with phenol-tris, phenol-chloroform (5:1) and chloroform-isoamyl alcohol (24:1) and a final precipitation with ethanol and sodium acetate (Garcia-Martinez et al., 2004).

tag: growth phase

value: Beginning of stationary phase

organism: Saccharomyces cerevisiae

value: Lalvin T73


title: stage 30

description: Gene expression at stage 25

source_name: stage 30, whole embryo

value: stage 30


title: High-grade serous ovarian cancer tissue Spo21T

source_name: Patient with high-grade ovarian cancer Spo21

value: high-grade ovarian cancer


title: Hybrid between S. cerevisiae and S. kudriavzevii VIN7 replicate A, fermentation at 28ºC

description: Gene expression of the hybrid between S. cerevisiae and S. kudriavzevii VIN7 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C. Replicate A


title: Peripheral blood Spo21N

value: Peripheral blood


title: Peripheral blood Spo20N


title: Hybrid between S. cerevisiae and S. kudriavzevii Lalvin W27 replicate C, fermentation at 28ºC

description: Gene expression of the hybrid between S. cerevisiae and S. kudriavzevii Lalvin W27 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C. Replicate C

source_name: yeast cells from wine fermentation at 12C

value: Lalvin W27


title: Hybrid between S. cerevisiae and S. kudriavzevii Lalvin VIN7 replicate C, fermentation at 28ºC

description: Gene expression of the hybrid between S. cerevisiae and S. kudriavzevii VIN7 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C. Replicate C


title: Hybrid between S. cerevisiae and S. kudriavzevii Lalvin W27 replicate B, fermentation at 28ºC

description: Gene expression of the hybrid between S. cerevisiae and S. kudriavzevii Lalvin W27 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C. Replicate B


title: stage 20

description: Gene expression at stage 15

source_name: stage 20, whole embryo

value: stage 20


title: stage 25

description: Gene expression at stage 20

source_name: stage 25, whole embryo

value: stage 25


title: Hybrid between S. cerevisiae and S. kudriavzevii Lalvin W27 replicate A, fermentation at 28ºC

description: Gene expression of the hybrid between S. cerevisiae and S. kudriavzevii Lalvin W27 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 28C. Replicate A


title: stage 15

description: Gene expression at stage 12

source_name: stage 15, whole embryo

value: stage 15


title: Hybrid between S. cerevisiae and S. kudriavzevii Lalvin VIN7 replicate C, fermentation at 12ºC

description: Gene expression of the hybrid between S. cerevisiae and S. kudriavzevii VIN7 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C. Replicate C


title: stage 12

description: Gene expression at stage 11

source_name: stage 12, whole embryo

value: stage 12


title: Peripheral blood Spo19N

source_name: Patient with high-grade ovarian cancer Spo19


title: stage 10.5

description: Gene expression at stage 10.5

source_name: stage 10.5, whole embryo

value: stage 10.5


title: stage 35

description: Gene expression at stage 30

source_name: stage 35, whole embryo

value: stage 35


title: High-grade serous ovarian cancer tissue Spo19T

value: Ovary


title: Hybrid between S. cerevisiae and S. kudriavzevii Lalvin VIN7 replicate B, fermentation at 12ºC

description: Gene expression of the hybrid between S. cerevisiae and S. kudriavzevii VIN7 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C. Replicate B


title: High-grade serous ovarian cancer tissue Spo18T

source_name: Patient with high-grade ovarian cancer Spo18


title: Peripheral blood Spo15N

source_name: Patient with high-grade ovarian cancer Spo15


title: stage 9

description: Gene expression at stage 9

source_name: stage 9, whole embryo

value: stage 9


title: Hybrid between S. cerevisiae and S. kudriavzevii VIN7 replicate A, fermentation at 12ºC

description: Gene expression of the hybrid between S. cerevisiae and S. kudriavzevii VIN7 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C. Replicate A


title: stage 8

description: Gene expression at stage 8

source_name: stage 8, whole embryo

value: stage 8


title: Hybrid between S. cerevisiae and S. kudriavzevii Lalvin W27 replicate C, fermentation at 12ºC

description: Gene expression of the hybrid between S. cerevisiae and S. kudriavzevii Lalvin W27 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C. Replicate C


title: Peripheral blood Spo14N

source_name: Patient with high-grade ovarian cancer Spo14


title: Hybrid between S. cerevisiae and S. kudriavzevii Lalvin W27 replicate A, fermentation at 12ºC

description: Gene expression of the hybrid between S. cerevisiae and S. kudriavzevii Lalvin W27 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C. Replicate A


title: High-grade serous ovarian cancer tissue Spo15T


title: 16-cell stage

description: Gene expression at the two-cell stage

source_name: 16-cell stage, whole embryo

value: 16-cell stage


title: Peripheral blood Spo18N


title: two-cell stage

description: Gene expression at the two-cell stage

source_name: two-cell stage, whole embryo

value: two-cell stage

value: whole embryo


title: unfertilized egg

description: Gene expression in unfertilized eggs

source_name: unfertilized egg, whole egg

value: unfertilized egg

value: whole egg


title: Set1_-

status: Public on Sep 04 2015

city: Boston

first: Yamicia

last: Connor

state: MA

address: 38 Dix Street Unit 1

institute: MIT

description: miRNA expression data from HUVEC cells grown in co-culture that have not received intercellular transfer from MDA-MB-231 cells as denoted by -CFSE signal

hyb_protocol: Affymetrix GeneChip® miRNA 3.0 Array was used. Hybridization was carried out using the Affymetrix GeneChip Hybridization Oven 640 for 42 hours.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing:
Microarray data analysis was carried out using the bioinformatics toolbox in MATLAB® (MathWorks®).
affymetrix-algorithm-name = rma : dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console

label_protocol: Labelling was carried out using the Affymetrix Flashtag Biotin HSR RNA labelling kit and standard protocol with a 1:500 dilution of ATP for Poly(A) Tailing.

growth_protocol: HUVEC cells (ATCC) were cultured on 0.1% gelatin in EBM-2 (Lonza) supplemented with bullet kit (Lonza) and 0.1% antibiotic/antimycotic (A/A) (Life Technologies).

extract_protocol: Total RNA isolation was carried out using the Ambion® mirVana™ RNA Isolation Kit (Life Technologies) per the manufacturer’s protocol and quantified using NanoDrop™ (Thermo Scientific)

treatment_protocol: DiL-Ac-LDL-labelled HUVEC and CFSE-labelled MDA-MB-231 cells were co-cultured in Matrigel™ using standard co-culture protocol for 36 hours. The cells were harvested and stained with PECAM-1 (1:25) (Abcam) and Alexa Fluor® 647 (1:100) (Life Technologies) secondary antibodies. Stained cells were then FACS sorted into PECAM-1 +/DiL-Ac-LDL+/CFSE+ and PECAM-1 +/DiL-Ac-LDL+/CFSE- populations, capturing HUVECs that did and did not receive nC mediated transfer. The sorted cells were then pelleted and snap frozen in liquid nitrogen.

tag: intracellular transfer

value: Endothelial cell co-culture


title: Set2_-


title: Set2_+

description: miRNA expression data from HUVEC cells grown in co-culture that have received intercellular transfer from MDA-MB-231 cells as denoted by +CFSE signal


title: High-grade serous ovarian cancer tissue Spo12T

source_name: Patient with high-grade ovarian cancer Spo12

value: high-grade ovarian cancer


title: Peripheral blood Spo13N

source_name: Patient with high-grade ovarian cancer Spo13

value: Peripheral blood


title: Set1_+


title: F12 Pfs16 24h Unlabeled

city: University Park

first: Heather

middle: J

last: Painter

state: Pennsylvania

address: Millennium Science Center

department: Biochemistry and Molecular Biology

institute: Penn State University

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

scan_protocol: Agilent G2505B Microarray Scanner. Images were quantified using Agilent Feature Extraction SoUnlabeledware (version 9.5.3.1).

data_processing: Agilent Feature Extraction SoUnlabeledware (v 9.5.3.1) was used for background subtraction and dye bias correction.  Princeton University Microarray Database (https://puma.princeton.edu/) was utilized for log2 ratio calculation. Data normalization is based upon a novel methodology as follows: 1) filter out probes that are AGILENT_CONTROL, *rRNA*, NOT_UNIQUE, and NO_HIT 2) Determine log2 ratio (normalized based on intensity and background subtraction) on a set of 47 expression profiles for each sample type (Total, Unlabeled, and Label).  3) smooth 48 time-course profiles of each probe. 4) set negative values to a small positive value. 5) fit non-negative least squares (NNLS) for each probe to estimate how much of the unlabeled and labeled gene expression cntribute to the total gene expression. 6) compute fitted values for Total sample by adding estimated unlabeled and estimated labeled expression.

organism: Plasmodium falciparum

source_name: 24h F12::Pfs16-FCU Unlabeled RNA

growth_protocol: P. falciparum strain 3D7 was highly synchronized parasites were grown under standard culturing conditions

extract_protocol: Starting at 0 hours post invasion, samples were harvested in Trizol for total RNA extraction every hour for 48 hours.

treatment_protocol: 50ml of standard culture was pulsed with 40uM 4-TU for 12 hours prior to Trizol RNA extraction.  This was repeated every 12 hours for 48 hours of intraerythrocytic development

tag: hours post invasion

tag: sample type

value: Total RNA

source_name: 3D7 Mixed Stage Reference Pool

tag: tag

value: Mixed stages


title: F12 CAM 24h Unlabeled

source_name: 24h F12::CAM-FCU Unlabeled RNA

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).


title: High-grade serous ovarian cancer tissue Spo14T


title: F12 Pfs16 0h Unlabeled

source_name: 0h F12::Pfs16-FCU Unlabeled RNA


title: F12 CAM 36h Unlabeled

source_name: 36h F12::CAM-FCU Unlabeled RNA


title: High-grade serous ovarian cancer tissue Spo10T

source_name: Patient with high-grade ovarian cancer Spo10


title: F12 CAM 0h Unlabeled

source_name: 0h F12::CAM-FCU Unlabeled RNA


title: Peripheral blood Spo11N

source_name: Patient with high-grade ovarian cancer Spo11


title: High-grade serous ovarian cancer tissue Spo11T


title: F12 CAM 12h Unlabeled

source_name: 12h F12::CAM-FCU Unlabeled RNA


title: High-grade serous ovarian cancer tissue Spo13T


title: E5 Pfs16 24h Unlabeled

source_name: 24h E5::Pfs16-FCU Unlabeled RNA


title: E5 Pfs16 12h Unlabeled

source_name: 12h E5::Pfs16-FCU Unlabeled RNA


title: Control

description: miRNA expression data from HUVEC cells grown in monoculture but using the same conditions as co-culture

value: Endothelial cell monoculture


title: E5 CAM 36h Unlabeled

source_name: 36h E5::CAM-FCU Unlabeled RNA


title: E5 Pfs16 0h Unlabeled

source_name: 0h E5::Pfs16-FCU Unlabeled RNA


title: E5 CAM 0h Unlabeled

source_name: 0h E5::CAM-FCU Unlabeled RNA


title: 3D7 Pfs 36h Unlabeled

source_name: 36h 3D7::Pfs16-FCU Unlabeled RNA


title: High-grade serous ovarian cancer tissue Spo7T

source_name: Patient with high-grade ovarian cancer Spo7


title: E5 CAM 12h Unlabeled

source_name: 12h E5::CAM-FCU Unlabeled RNA


title: 3D7 Pfs 12h Unlabeled

source_name: 12h 3D7::Pfs16-FCU Unlabeled RNA


title: F12 Pfs16 12h Unlabeled

source_name: 12h F12::Pfs16-FCU Unlabeled RNA

source_name: 3D7 Mixed Stage Reference Pool


title: Hybrid between S. cerevisiae and S. kudriavzevii Lalvin W27 replicate B, fermentation at 12ºC

description: Gene expression of the hybrid between S. cerevisiae and S. kudriavzevii Lalvin W27 with respect to the reference strain S. cerevisiae Lalvin T73. Samples from wine fermentation at 12C. Replicate B

source_name: yeast cells from wine fermentation at 12C

value: Lalvin W27

value: Beginning of stationary phase

value: Lalvin T73


title: 3D7 Pfs 24h Unlabeled

source_name: 24h 3D7::Pfs16-FCU Unlabeled RNA


title: F12 Pfs16 36h Unlabeled

source_name: 36h F12::Pfs16-FCU Unlabeled RNA


title: Peripheral blood Spo12N

source_name: Patient with high-grade ovarian cancer Spo12


title: 3D7 CAM 36h Unlabeled

source_name: 36h 3D7::CAM-FCU Unlabeled RNA


title: High-grade serous ovarian cancer tissue Spo8T

source_name: Patient with high-grade ovarian cancer Spo8

value: Ovary


title: 3D7 CAM 24h Unlabeled

source_name: 24h 3D7::CAM-FCU Unlabeled RNA


title: 3D7 CAM 12h Unlabeled

source_name: 12h 3D7::CAM-FCU Unlabeled RNA


title: 3D7 Pfs 0h Unlabeled

source_name: 0h 3D7::Pfs16-FCU Unlabeled RNA


title: Peripheral blood Spo8N


title: E5 Pfs16 36h Unlabeled

source_name: 36h E5::Pfs16-FCU Unlabeled RNA


title: 3D7 CAM 0h Unlabeled

source_name: 0h 3D7::CAM-FCU Unlabeled RNA


title: F12 Pfs16 12h Labeled

source_name: 12h F12::Pfs16-FCU Labeled RNA


title: F12 Pfs16 24h Labeled

source_name: 24h F12::Pfs16-FCU Labeled RNA


title: Peripheral blood Spo9N

source_name: Patient with high-grade ovarian cancer Spo9


title: F12 Pfs16 36h Labeled

source_name: 36h F12::Pfs16-FCU Labeled RNA


title: High-grade serous ovarian cancer tissue Spo9T


title: F12 CAM 36h Labeled

source_name: 36h F12::CAM-FCU Labeled RNA


title: F12 CAM 24h Labeled

source_name: 24h F12::CAM-FCU Labeled RNA

source_name: 3D7 Mixed Stage Reference Pool


title: F12 CAM 0h Labeled

source_name: 0h F12::CAM-FCU Labeled RNA


title: F12 CAM 12h Labeled

source_name: 12h F12::CAM-FCU Labeled RNA


title: E5 Pfs16 36h Labeled

source_name: 36h E5::Pfs16-FCU Labeled RNA


title: Peripheral blood Spo7N

source_name: Patient with high-grade ovarian cancer Spo7


title: Peripheral blood Spo1N

source_name: Patient with high-grade ovarian cancer Spo1


title: E5 Pfs16 12h Labeled

source_name: 12h E5::Pfs16-FCU Labeled RNA


title: High-grade serous ovarian cancer tissue Spo3T

source_name: Patient with high-grade ovarian cancer Spo3


title: Peripheral blood Spo4N

source_name: Patient with high-grade ovarian cancer Spo4


title: E5 CAM 24h Labeled

source_name: 24h E5::CAM-FCU Labeled RNA

value: Labeled RNA


title: E5 CAM 36h Labeled

source_name: 36h E5::CAM-FCU Labeled RNA


title: E5 Pfs16 0h Labeled

source_name: 0h E5::Pfs16-FCU Labeled RNA


title: E5 CAM 0h Labeled

source_name: 0h E5::CAM-FCU Labeled RNA


title: E5 CAM 12h Labeled

source_name: 12h E5::CAM-FCU Labeled RNA


title: 3D7 CAM 12h Labeled

source_name: 12h 3D7::CAM-FCU Labeled RNA


title: E5 Pfs16 24h Labeled

source_name: 24h E5::Pfs16-FCU Labeled RNA


title: 3D7 CAM 0h Labeled

source_name: 0h 3D7::CAM-FCU Labeled RNA


title: High-grade serous ovarian cancer tissue Spo4T


title: Peripheral blood Spo10N

source_name: Patient with high-grade ovarian cancer Spo10


title: 3D7 CAM 36h Labeled

source_name: 36h 3D7::CAM-FCU Labeled RNA

source_name: 3D7 Mixed Stage Reference Pool


title: 3D7 Pfs16 24h Labeled

source_name: 24h 3D7::Pfs16-FCU Labeled RNA


title: High-grade serous ovarian cancer tissue Spo1T


title: 3D7 Pfs16 36h Labeled

source_name: 36h 3D7::Pfs16-FCU Labeled RNA


title: 3D7 Pfs16 0h Labeled

source_name: 0h 3D7::Pfs16-FCU Labeled RNA


title: 3D7 Pfs16 12h Labeled

source_name: 12h 3D7::Pfs16-FCU Labeled RNA


title: 3D7 CAM 24h Labeled

source_name: 24h 3D7::CAM-FCU Labeled RNA


title: E5 CAM 24h Unlabeled

source_name: 24h E5::CAM-FCU Unlabeled RNA


title: siAKT 24hr R5 PRB3

city: Chicago

first: Irene

middle: Inkyung

last: Lee

state: IL

address: 303 E. Superior St, Lurie 4-250

department: OB/GYN

institute: Northwestern University

data_processing: Data were processed through the use of Ingenuity iReport. Variance Stabilizing Transformation was applied to data prior to quantile normalization.

source_name: PRB-Ishikawa cells, siAKT, R5020

label_protocol: Standard Illumina labeling protocol

growth_protocol: PRB-Ishikawa cells were maintained in DMEM/F12 supplemented with 10% FBS, sodium pyruvate, penicillin/streptomycin, hygromycin, and G418.

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

treatment_protocol: The cells were transfected with either siCtrl or siAkt1, siAkt2, and siAkt3 (siAkt). Cells were then serum starved overnight and then treated with either Ethanol Vehicle Control or 10 nM R5020 for 24 hrs.

tag: cell line

value: PRB-Ishikawa

value: endometrial cancer


title: HM4

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Gene expression in lungs of male rat kept in hypobaric hypoxic conditions with MCT

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two pups were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 11.5.1.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.

source_name: Hypobaric hypoxic conditions with MCT_Replicate 4

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Male Sprague-Dawley rats (150-175g) were obtained from Charles River Wilmington, MA. Rats were allowed to acclimatize in the animal facility for 5 days, and had free access to laboratory chow and water. The rats were kept in the Animal facility maintained at 22o C and 12 hours each of light and dark cycle. The Protocols were approved by the Institutional Animal Care and Use Committee at New York Medical College,  and conform to the guiding principles for the use and care of laboratory animals of the American Physiological Society, and the National Institutes of Health.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Rats were divided into 4 groups: CO, Control rats maintained in room air; CM, rats received a single subcutaneous injection of monocrotaline (MCT 40 mg/kg), and kept in room air. HO, rats subjected to hypobaric hypoxia (atmospheric pressure 380 mmHg); HM, rats received MCT 40 mg/kg and were subjected to hypobaric hypoxia starting on day1. The hypoxia chamber was opened twice per week for 15 min to weigh the rats, replenish food and water, and to provide clean bedding similar to the other rats in room air. At the end of 4 weeks, these rats were studied.

tag: Sex

value: female

value: Sprague-Dawley

tag: tissue

value: lungs

value: Adult

tag: atmospheric condition

value: hypobaric hypoxic

value: with MCT


title: siAKT 24hr R5 PRB2


title: siAKT 24hr VC PRB1

source_name: PRB-Ishikawa cells, siAKT, Ethanol


title: siAKT 24hr R5 PRB1


title: siAKT 24hr VC PRB3


title: CM3

description: Gene expression in lungs of male rat kept in normal atmospheric conditions with MCT

source_name: Normal atmospheric conditions with MCT_Replicate 3

value: male

tag: strain

value: normal

tag: treatment


title: siCTRL 24hr R5 PRB1

source_name: PRB-Ishikawa cells, siCTRL, R5020


title: Peripheral blood Spo3N

description: Hybridized to Genome-Wide Human SNP Array 6.0

source_name: Patient with high-grade ovarian cancer Spo3

tag: disease state

value: high-grade ovarian cancer

value: Peripheral blood


title: siCTRL 24hr R5 PRB3

tag: cell type


title: siAKT 24hr VC PRB2


title: siCTRL 24hr R5 PRB2


title: HM1

source_name: Hypobaric hypoxic conditions with MCT_Replicate 1


title: F12 Pfs16 0h Labeled

source_name: 0h F12::Pfs16-FCU Labeled RNA

value: Total RNA

value: Mixed stages


title: CM4

source_name: Normal atmospheric conditions with MCT_Replicate 4


title: CM2

source_name: Normal atmospheric conditions with MCT_Replicate 2


title: HO4

description: Gene expression in lungs of male rat kept in hypobaric hypoxic conditions without MCT

source_name: Hypobaric hypoxic conditions without MCT_Replicate 4

value: without MCT


title: CM1

source_name: Normal atmospheric conditions with MCT_Replicate 1


title: HM2

source_name: Hypobaric hypoxic conditions with MCT_Replicate 2


title: MM231 cells Tx COMBO, biological rep1

city: Pittsburgh

first: Yi

last: Huang

address: 204 Craft Ave

department: Pharmacology & Chemical Biology

institute: University of Pittsburgh Cancer Institute

description:
combo1
MDA-MB-231 cells, treated with 5uM SAHA + 2.5mM Pargyline for 24 hours, biological replicate 1

hyb_protocol: cRNA was hybridized to U133A 2.0 arrays (Affymetrix, Santa Clara, CA)

scan_protocol: cRNA synthesis and labeling, hybridization, and scanning were performed by the University of Pittsburgh Cancer Biomarkers Facility

data_processing: The data were processed as RMA files (Affymetrix Robust Multi-Array Average) in which the raw intensity data were background corrected, log2 transformed, and then quantile normalized according to Affymetrix recommendations. The Student’s t-test was used to determine the statistical differences between various experimental and control groups. Microarray statistical tests were performed using Significance Analysis of Microarrays software (SAM version 3.09c), which is designed to reduce the risk of Type 1 errors due to multiple testing.

label_protocol: cRNA synthesis and labeling was performed using the Ambion MessageAmp Premier Kit (Life Technologies)

growth_protocol: normal culturing conditions for MDA-MB-231

extract_protocol: QIAgen RNeasy Mini (Animal Cells Spin protocol, w/DNase I digest performed on homogenized lysate prior to applying lysate to column for purification)

treatment_protocol: MDA-MB-231 cells were treated for 24 hours with 5uM SAHA (Vorinostat), 2.5mM Pargyline, 5uM SAHA + 2.5mM Pargyline (combination of both drugs), or vehicle (DMSO).

value: breast cancer cell line

tag: treated with

value: 5 micromolar SAHA (suberanilohydroxamic acid) + 2.5 millimolar Pargyline for 24hrs


title: CO4

description: Gene expression in lungs of male rat kept in normal atmospheric conditions without MCT

source_name: Normal atmospheric conditions without MCT_Replicate 4


title: siCTRL 24hr VC PRB2

source_name: PRB-Ishikawa cells, siCTRL, Ethanol

value: PRB-Ishikawa


title: siCTRL 24hr VC PRB1

value: endometrial cancer


title: siCTRL 24hr VC PRB3


title: HO3

source_name: Hypobaric hypoxic conditions without MCT_Replicate 3

value: female


title: MM231 cells Tx COMBO, biological rep2

description:
combo2
MDA-MB-231 cells, treated with 5uM SAHA + 2.5mM Pargyline for 24 hours, biological replicate 2


title: HO2

source_name: Hypobaric hypoxic conditions without MCT_Replicate 2

value: Sprague-Dawley


title: MM231 cells Tx Pargyline, biological rep3

description:
Pargyline3
MDA-MB-231 cells, treated with 2.5mM Pargyline for 24 hours, biological replicate 3

value: 2.5 millimolar Pargyline for 24 hrs


title: HO1

source_name: Hypobaric hypoxic conditions without MCT_Replicate 1

value: lungs

value: Adult


title: CO3

source_name: Normal atmospheric conditions without MCT_Replicate 3


title: MM231 cells Tx DMSO, biological rep2

description:
control2
MDA-MB-231 cells, treated with DMSO (vehicle) for 24 hrs, biological replicate 2

value: DMSO (vehicle) for 24 hrs


title: Betacell.NOD.12wk#2

first: James

last: Mohan

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization).

source_name: Pancreas

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: beta cells from isolated pancreatic islets

tag: age

value: 12 Weeks Old

tag: exclusion markers

value: Dapi, CD45

tag: genetic background

value: NOD

tag: phenotype markers

tag: separation method

value: FACSAria

tag: gender

value: Female


title: MM231 cells Tx Pargyline, biological rep2

description:
Pargyline2
MDA-MB-231 cells, treated with 2.5mM Pargyline for 24 hours, biological replicate 2


title: CO2

source_name: Normal atmospheric conditions without MCT_Replicate 2

value: male

tag: developmental stage

value: normal

value: without MCT


title: Betacell.NOD.12wk#1


title: MM231 cells Tx Pargyline, biological rep1

description:
Pargyline1
MDA-MB-231 cells, treated with 2.5mM Pargyline for 24 hours, biological replicate 1

value: breast cancer cell line


title: CO1

source_name: Normal atmospheric conditions without MCT_Replicate 1


title: MM231 cells Tx DMSO, biological rep1

description:
control1
MDA-MB-231 cells, treated with DMSO (vehicle) for 24 hrs, biological replicate 1


title: MM231 cells Tx SAHA, biological rep1

description:
SAHA1
MDA-MB-231 cells, treated with 5uM SAHA for 24 hours, biological replicate 1

value: 5 micromolar SAHA (suberanilohydroxamic acid) for 24 hrs


title: Betacell.NOD.4wk#2

value: 4 Weeks Old


title: MM231 cells Tx DMSO, biological rep3

description:
control3
MDA-MB-231 cells, treated with DMSO (vehicle) for 24 hrs, biological replicate 3


title: Kidney_Roundup_rep2

city: London

first: Matthew

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

country: United Kingdom

institute: King's College London

hyb_protocol: Hybridisation cocktails were prepared using 5.5ug cDNA as described in the Eukaryotic Array manual from Affymetrix, using the Hybridisation, Wash and Stain (HWS) kit (Affymetrix)

scan_protocol: Arrays were scanned using the GCS3000 7G scanner (Affymetrix) following manufacturer's protocols.

data_processing: CEL files were imported into Expression Console software (Affymetrix) and normalised using RMA-sketch (gene-level).

source_name: Kidney

label_protocol: RNA was processed using the Ambion WT Expression kit and Affymetrix WT Terminal Labelling kit.

extract_protocol: Frozen kidney samples were homogenised and RNA extracted using MagMAX-96 for Micorarrays Kit (AM1839). The spin procedure was followed. RNA was eluted in 50ul of elution buffer.

treatment_protocol: Kidneys were extracted at autopsy and half of the organ was snap frozen for RNA subsequent RNA isolation. Samples were stored at -80 until extraction.

value: female

value: Sprague-Dawley

value: Kidney

tag: experimental group

value: Roundup

tag: age at death (days)


title: MM231 cells Tx SAHA, biological rep2

description:
SAHA2
MDA-MB-231 cells, treated with 5uM SAHA for 24 hours, biological replicate 2

tag: cell line


title: Kidney_Roundup_rep5

tag: tissue


title: MM231 cells Tx COMBO, biological rep3

description:
combo3
MDA-MB-231 cells, treated with 5uM SAHA + 2.5mM Pargyline for 24 hours, biological replicate 3

value: 5 micromolar SAHA (suberanilohydroxamic acid) + 2.5 millimolar Pargyline for 24hrs


title: Kidney_Roundup_rep7


title: Betacell.NOD.4wk#1

value: beta cells from isolated pancreatic islets


title: Kidney_Control_rep10

value: control


title: Kidney_Roundup_rep6


title: Kidney_Roundup_rep1


title: Kidney_Roundup_rep9


title: Kidney_Control_rep6


title: Kidney_Control_rep7


title: Kidney_Roundup_rep8


title: Kidney_Control_rep1


title: Kidney_Roundup_rep3


title: Kidney_Control_rep2


title: Kidney_Control_rep8


title: Kidney_Control_rep3


title: Kidney_Control_rep5


title: Kidney_Roundup_rep4


title: Kidney_Control_rep9


title: Kidney_Control_rep4


title: HM3

source_name: Hypobaric hypoxic conditions with MCT_Replicate 3

tag: Sex

value: lungs

value: Adult

tag: atmospheric condition

value: hypobaric hypoxic

value: with MCT


title: MM231 cells Tx SAHA, biological rep3

description:
SAHA3
MDA-MB-231 cells, treated with 5uM SAHA for 24 hours, biological replicate 3


title: Liver_Roundup_rep10

source_name: Liver

extract_protocol: Frozen liver samples were homogenised and RNA extracted using MagMAX-96 for Micorarrays Kit (AM1839). The spin procedure was followed. RNA was eluted in 50ul of elution buffer.

treatment_protocol: Livers were extracted at autopsy and half of the organ was snap frozen for RNA subsequent RNA isolation. Samples were stored at -80 until extraction.

tag: strain

value: Liver


title: Liver_Roundup_rep7


title: Liver_Roundup_rep9


title: IKZF1_5

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

description: Ikzf1+/-, replicate 5

hyb_protocol: Hybridization was carried out in an Agilent oven at 65°C for 40 hours at 20 rpm; after hybridization, slides were washed sequentially according to manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1) with protocol CGH_105_Jan09 and LOWESS normalization.

source_name: non-leukemic  bone marrow

label_protocol: 1.5μg of genomic DNA was labeled using the Agilent ULS Labeling kit

growth_protocol: DNA was extracted from GFP+ leukemic bone marrow cells derived from wildtype or Ikzf1-altered mice

extract_protocol: Phenol-chloroform

value: stage-matched bone marrow

tag: disease state

value: non-leukemic

source_name: leukemic bone marrow

value: Ikzf1+/- primary tumor sample

tag: genotype

value: leukemic


title: Liver_Roundup_rep8


title: IKZF1_1

description: Ikzf1+/-, replicate 1


title: Liver_Roundup_rep6


title: BMDC_CpGtreated_rep4

city: Portland

first: Evan

middle: F.

last: Lind

state: OR

address: Mail Code L220, 3181 SW Sam Jackson Park Road

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

description:
Whole RNA with miRNA
BMDC+CpG4
DC4 CpG_S01_1_1_

hyb_protocol: Agilent miRNA Complete Labeling and Hyb Kit

scan_protocol: scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

data_processing:
GeneView intensity files were imported into R, values less than 0.01 were set to 0.01. Pearson correlations were calculated and outputted into correlation file MDS plot: pearson_plot_filter.png Hierarchical clustering of samples based on pearson correlation: 'HCL_sample_filter.png' Unsupervised Hierarchical clustering result: 'HCL_filter.png' linear fit was done by limma package from R/bioconductor.
FilteredIntensities_mirna_dc.txt is linked as a supplementary file on the Series record.

source_name: Bone marrow derived dendritic cells CpG treated overnight

growth_protocol: Bone marrow was flushed from tibias and femurs of mice with HBSS. Bone marrow cells were cultured at 2x106 cells/ml in 10 ml non-tissue culture treated dishes in RPMI 1640 containing 10% LPS-free FBS, Penicillin:streptomycin glutamine 2-mercaptoethanol (cRPMI), with 40ng/ml murine GM-CSF (Peprotech). On day 3 of cultures 10ml of fresh media was added also containing 40ng/ml GM-CSF. On days 6 and 8, 10ml of media was removed and centrifuged to collect cells, which were resuspended in 10ml fresh media containing GM-CSF and were added back to dishes. Non-adherent cells were isolated on day 9. DCs were plated in 24-well plates at 2x106 cells/ml in 1ml of cRPMI with or without the class B CpG ODN1826 (ACGT DNA Technologies corporation, Toronto, ON, Canada) at 10μM final concentration overnight.

extract_protocol: mirVana miRNA isolation kit

treatment_protocol: Cells were treated with CpG or control (PBS alone)

tag: cell type

value: BMDC

tag: agent

value: CpG


title: BMDC_CpGtreated_rep3

description:
Whole RNA with miRNA
BMDC+CpG3
DC3 CpG_S01_2_4_

label_protocol: Agilent miRNA Complete Labeling and Hyb Kit


title: BMDC_CpGtreated_rep1

description:
Whole RNA with miRNA
BMDC+CpG1
DC1 CpG_S01_1_4_


title: BMDC_CpGtreated_rep2

description:
Whole RNA with miRNA
BMDC+CpG2
DC2 CpG_S01_2_2_


title: Liver_Roundup_rep5

value: female

value: Sprague-Dawley


title: IKZF1_4

description: Ikzf1+/-, replicate 4


title: Liver_Control_rep6


title: Liver_Roundup_rep2

value: Roundup


title: BMDC_untreated_rep4

description:
Whole RNA with miRNA
BMDC4
DC4_S01_1_2_

source_name: Bone marrow derived dendritic cells unstimulated


title: Liver_Control_rep5


title: Liver_Control_rep7


title: IKZF1_2

description: Ikzf1+/-, replicate 2


title: IKZF1_3

description: Ikzf1+/-, replicate 3


title: Liver_Control_rep1


title: Liver_Control_rep2


title: Liver_Control_rep10


title: Liver_Roundup_rep3


title: Liver_Control_rep3


title: Liver_Control_rep8


title: Liver_Roundup_rep4


title: BMDC_untreated_rep3

description:
Whole RNA with miRNA
BMDC3
DC3_S01_2_3_


title: BMDC_untreated_rep1

description:
Whole RNA with miRNA
BMDC1
DC1_S01_1_3_


title: BMDC_untreated_rep2

description:
Whole RNA with miRNA
BMDC2
DC2_S01_2_1_


title: WT_5

description: Ikzf1+/+, replicate 5

value: Ikzf1+/+ primary tumor sample


title: Liver_Control_rep9


title: Liver_Control_rep4


title: WT_4

description: Ikzf1+/+, replicate 4


title: WT_2

description: Ikzf1+/+, replicate 2


title: Liver_Roundup_rep1


title: HCT116_TET1KD_rep2

city: Tokyo

first: Yotaro

last: Kudo

address: 7-3-1 Hongo, Bunkyo-ku

department: Gastroenterology

institute: University of Tokyo

description: Gene expression after transfection of TET1 siRNA in HCT116 cells

hyb_protocol: 10 micrograms of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controlled by use of the GeneChip® Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.

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

data_processing: GeneChip analysis was performed using the Affymetrix GeneChip® Operating Software v1.4. The average values were scaled to 100 so that all chips could be directly compared.

source_name: Total RNA extracted from human colorectal cancer cell line HCT116 transfected with TET1 siRNA, replicate 2

label_protocol: In vitro transcription was performed on all of cDNA using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin column (QIAGEN). The cRNA was fragmented by metal-induced hydrolysis.

growth_protocol: Cells were grown in McCoy's 5A medium with 10% fetal bovine serum, maintained at 37C in 5% CO2 in a humidified environment.

extract_protocol: Total RNA was extracted from cells with NucleoSpin RNA kit (Takara Bio.) following manufacturer’s instructions, and  3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

treatment_protocol: siRNA was transfected using Lipofectamin RNAiMAX reagent (Invitrogen) according to the manufacturer's protocol.

tag: transfected sirna

value: TET1 siRNA


title: HCT116_TET1KD_rep1

source_name: Total RNA extracted from human colorectal cancer cell line HCT116 transfected with TET1 siRNA, replicate 1


title: WT_1

description: Ikzf1+/+, replicate 1


title: HCT116_Ctrl_rep2

description: Gene expression after transfection of control siRNA in HCT116 cells

source_name: Total RNA extracted from human colorectal cancer cell line HCT116 transfected with control siRNA, replicate 2

value: control siRNA


title: ATF4 mKO mouse 1

status: Public on Sep 03 2015

city: Iowa City

first: Scott

middle: M

last: Ebert

state: IA

address: 500 Newton Rd

department: Int Med

institute: University of Iowa

description: skeletal muscle RNA

hyb_protocol: Amplified and labeled cRNA was quantified (Ribogreen assay) and hybridized to Mouse Ref-8 version 2.0 BeadChip Arrays (Illumina) overnight at 58°C. Following hybridization, arrays were washed, blocked, stained, and dried (Little Dipper Processor).

scan_protocol: Arrays were scanned with an iScan reader, and data were extracted and analyzed with BeadStudio Software (Illumina).

data_processing: Data was processed using Bioconductor Software with VST transformation and RSN normalization.

source_name: quadriceps femoris

label_protocol: RNA was then amplified and labeled (Ambion TotalPrep Kit), and cDNA was synthesized using robotic-assisted magnetic capture. Using the cDNA template, biotinylated cRNA was produced via an in vitro transcription reaction.

extract_protocol: Skeletal muscle RNA was extracted using TRIzol solution (Invitrogen) and then purified using the RNeasy kit and RNase Free DNase Set (Qiagen).

treatment_protocol: Quadriceps femoris muscles were harvested from 22-month-old muscle-specfic ATF4 knockout (ATF4 mKO) mice and littermate controls.  mRNA levels in ATF4 mKO muscles were normalized to levels in littermate control muscles.

tag: age

value: 22 months old

value: male

tag: genotype/variation

value: ATF4 mKO


title: WT_3

description: Ikzf1+/+, replicate 3


title: ATF4 mKO mouse 2

description: skeletal muscle RNA


title: Control mouse 8

description: skeletal muscle RNA

value: control


title: ATF4 mKO mouse 5

description: skeletal muscle RNA


title: ATF4 mKO mouse 7

description: skeletal muscle RNA


title: Control mouse 3

description: skeletal muscle RNA


title: ATF4 mKO mouse 8

description: skeletal muscle RNA


title: Control mouse 4

description: skeletal muscle RNA


title: HCT116_Ctrl_rep1

source_name: Total RNA extracted from human colorectal cancer cell line HCT116 transfected with control siRNA, replicate 1


title: ATF4 mKO mouse 6

description: skeletal muscle RNA


title: ATF4 mKO mouse 4

description: skeletal muscle RNA


title: Control mouse 6

description: skeletal muscle RNA


title: Control mouse 5

description: skeletal muscle RNA


title: ATF4 mKO mouse 3

description: skeletal muscle RNA


title: Control mouse 2

description: skeletal muscle RNA


title: UA diet mouse 1

description: skeletal muscle RNA

treatment_protocol: Weight-matched cohorts of 22-month-old male C57BL/6 mice were provided ad libitum access to standard chow (control) or standard chow supplemented with 0.27% ursolic acid (UA) or 0.05% tomatidine (TM) for 2 months.  After the 2 month treatment period, quadriceps femoris muscles were harvested.  mRNA levels in muscles harvested from ursolic acid or tomatidine fed mice were normalized to levels in muscles fed control diet.

value: 24 months old

tag: diet

value: standard chow supplemented with 0.27% ursolic acid (UA) for 2 months


title: Control mouse 1

description: skeletal muscle RNA


title: UA diet mouse 6

description: skeletal muscle RNA


title: UA diet mouse 3

description: skeletal muscle RNA


title: UA diet mouse 5

description: skeletal muscle RNA


title: UA diet mouse 4

description: skeletal muscle RNA


title: Control mouse 7

description: skeletal muscle RNA


title: UA diet mouse 2

description: skeletal muscle RNA


title: TM diet mouse 4

description: skeletal muscle RNA

value: standard chow supplemented with 0.05% tomatidine (TM) for 2 months


title: TM diet mouse 5

description: skeletal muscle RNA


title: TM diet mouse 3

description: skeletal muscle RNA


title: Control diet mouse 5

description: skeletal muscle RNA

value: standard chow


title: MCF10A/ErbB2*, 3D, rep3

first: Jiyang

last: Yu

address: 262 Danny Thomas Place, MS 1135

department: Computational Biology

institute: St. Jude Children's Research Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: R packcage lumi, V2.8., RSN and VSN normalization

source_name: MCF10A/ErbB2*, 3D

label_protocol: Biotinilated with Illumina total Prep RNA amplification kit (Ambion#AMIL1791)

extract_protocol: RNA was extracted with RNaesy kit (Qiagen)


title: TM diet mouse 2

description: skeletal muscle RNA


title: Control diet mouse 4

description: skeletal muscle RNA


title: Control diet mouse 2

description: skeletal muscle RNA


title: MCF10A/ErbB2*, 3D, rep6


title: MCF10A/ErbB2*, 2D, rep4

source_name: MCF10A/ErbB2*, 2D


title: MCF10A/ErbB2*, 2D, rep5


title: MCF10A/ErbB2*, 3D, rep4


title: Control diet mouse 1

description: skeletal muscle RNA


title: Control diet mouse 3

description: skeletal muscle RNA


title: MCF10A/ErbB2*, 3D, rep5


title: MCF10A/ErbB2*, 3D, rep1


title: MCF10A/ErbB2*, 2D, rep2


title: MCF10A/ErbB2*, 2D, rep3


title: MCF10A/ErbB2*, 3D, rep2


title: MCF10A/ErbB2*, 2D, rep1


title: MCF10A/ErbB2*, 2D, rep6


title: MCF10A WT, 2D, rep3

source_name: MCF10A WT, 2D


title: MCF10A WT, 2D, rep2


title: MCF10A WT, 2D, rep5


title: MCF10A WT, 3D, rep3

source_name: MCF10A WT, 3D


title: MCF10A WT, 3D, rep1


title: MCF10A WT, 3D, rep2


title: MCF10A WT, 3D, rep4


title: MCF10A WT, 2D, rep6


title: MCF10A WT, 2D, rep1


title: MCF10A WT, 3D, rep5


title: MCF10A WT, 2D, rep4


title: peripheral blood PMN, replicate 3

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

description: steady-state

hyb_protocol: Hybridization to chips (Affymetrix Human Genome U133 Plus 2.0 arrays) was performed according to the Affymetrix Expression Analysis Technical Manual.

scan_protocol: Image scanning was performed according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were RMA normalized in R and Bioconductor

source_name: peripheral blood

label_protocol: For each blood cell subtype, 25 ng total RNA was labeled using a two-cycle target labeling protocol and hybridized to arrays.

extract_protocol: For each cell subtype, 8 mL whole blood was drawn into Vacutainer CPT cell preparation tubes that contained sodium citrate and Ficoll (Becton–Dickinson, NJ, USA). 400 mL of RosetteSep Ab cocktail was added to each tube and incubated for 20 min at room temperature. After incubation, the blood collected in the CPT tubes was centrifuged for 20 min at 1800g. The desired cells, not labeled with antibody, were collected from the plasma:Ficoll interface and washed once with PBS and the RNA was isolated using Trizol reagent. For the separation of PMNs, 6 mL sodium citrate–anti-coagulated venous blood was carefully layered on 3 mL leukocyte separation media. After a 700g centrifugation for 30 min at room temperature, the “mononuclear” layer together with fluid within 0.5 cm of this layer was aspirated and discarded, while the “granulocyte” layer was transferred to a new tube and washed once with phosphate-buffered saline.

treatment_protocol: Blood was drawn from three healthy donors for all cell subsets. The donors were healthy, ages 32, 33, and 59. Two were male. Subsets of mononuclear cells including CD4+ T cells, CD8+ T cells, CD19+ B cells, CD56+ NK cells, and CD14+ monocytes were enriched using the RosetteSep negative selection method (StemCell Technologies, BC, Canada).

tag: diagnosis

value: healthy

value: polymorphonuclear cells

value: peripheral blood


title: peripheral blood CD4+ T cells, replicate 3

description: steady-state

value: CD4+ T cells


title: peripheral blood CD14+ monocytes, replicate 3

description: steady-state

value: CD14+ monocytes


title: peripheral blood CD8+ T cells, replicate 2

description: steady-state

value: CD8+ T cells


title: 25T

city: Cambridge

first: Muhammad

middle: Abdullah

last: Alvi

address: Addenbrooke's site

institute: University of Cambridge

scan_protocol: Standard Illumina scanning protocol using iScan

data_processing: Non-normalized and average normalised (background subtracted) using GenomeStudio v2011.1 9

label_protocol: Standard Illumina protocol

extract_protocol: RNA was extracted using RNeasy FFPE Kit (Qiagen, UK)

tag: source

value: FFPE tissue blocks

tag: pathology

value: Small bowel cancer tissue from surgical resection


title: peripheral blood CD19+ B cells, replicate 3

description: steady-state

value: CD19+ B cells


title: 23T


title: 20T


title: 26T


title: 28T


title: 19T


title: peripheral blood CD8+ T cells, replicate 3

description: steady-state


title: 22T


title: 27T


title: peripheral blood CD8+ T cells, replicate 1

description: steady-state


title: peripheral blood CD56+ NK cells, replicate 3

description: steady-state

value: CD56+ NK cells


title: peripheral blood CD56+ NK cells, replicate 2

description: steady-state


title: peripheral blood PMN, replicate 2

description: steady-state


title: peripheral blood CD14+ monocytes, replicate 2

description: steady-state


title: peripheral blood CD14+ monocytes, replicate 1

description: steady-state


title: peripheral blood CD4+ T cells, replicate 2

description: steady-state


title: 24T


title: 18T


title: peripheral blood PMN, replicate 1

description: steady-state


title: peripheral blood CD56+ NK cells, replicate 1

description: steady-state


title: TM diet mouse 1

description: skeletal muscle RNA

value: male


title: 21T


title: peripheral blood CD4+ T cells, replicate 1

description: steady-state


title: peripheral blood CD19+ B cells, replicate 1

description: steady-state


title: peripheral blood CD19+ B cells, replicate 2

description: steady-state


title: 17T


title: 16T


title: 6T


title: 13T


title: 8T


title: 15T


title: 25N

value: Normal small bowel epithelium from a cancer patient


title: 3T


title: 12T


title: 23N


title: 20N


title: 24N


title: 7T


title: 2T


title: 22N


title: 15N


title: 18N


title: 19N


title: 13N


title: 14N


title: 14T


title: 17N


title: 16N


title: 11T


title: 11N