title: Whole right lung day 56 post sham surgery

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

hyb_protocol: Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight.  Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

scan_protocol: Scanning is carried out on a Affymetrix GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.

data_processing: All 21 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.

source_name: whole right lung

label_protocol: In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.

extract_protocol: For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Concentrations may also be determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).

tag: Sex

value: Male

tag: strain

value: Sham surgery

tag: comment

value: microarray hybridization data 06/06/2011

value: Whole right lung

value: day 56 post sham surgery


title: Tumor cells (MiaPaCa2) treated with naive stellate cells (PSC), 5h

status: Public on Aug 09 2013

type: RNA

city: Heidelberg

first: Matt

middle: Zbigniew

last: Rogon

address: Meyerhofstrasse 1

department: SCB

country: Germany

institute: EMBL

description: MiaPaca2 post naive PSC-treatment

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

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

data_processing: The data were processed with R using RMA normalization procedure (justRMA package), annotated with the corresponding library (hgu133plus2.db), and extracted in both unfiltered (normalized, complete set), and filtered (IQR filtering 0.35).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MiaPaCa2 cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: regular frowth to 70% confuence at 37oC

extract_protocol: Qiagen RNA kit extraction according to manufacturer's protocol

treatment_protocol: Stellate-cell supernatant was added 24, 7,6,5,4,3,2, and  1hour prior harvest

tag: pancreatic tumor cell line


title: Tumor cells (MiaPaCa2) treated with naive stellate cells (PSC), 6h

description: MiaPaca2 post naive PSC-treatment


title: Tumor cells (MiaPaCa2) treated with naive stellate cells (PSC), 4h

description: MiaPaca2 post naive PSC-treatment


title: Whole right lung day 14 post-left pneumonectomy

country: USA

label: Biotin

organism: Mus musculus

tag: treatment

value: Left pneumonectomy

tag: tissue

tag: time

value: day 14 post-left pneumonectomy


title: Whole right lung day 7 post-left pneumonectomy

value: day 7 post-left pneumonectomy


title: Whole right lung day 56 post-left pneumonectomy

value: day 56 post-left pneumonectomy


title: Tumor cells (MiaPaCa2) treated with naive stellate cells (PSC), 1h

description: MiaPaca2 post naive PSC-treatment


title: Whole right lung day 0 pre-left pneumonectomy

value: No pneumonectomy

value: day 0 pre-left pneumonectomy


title: Primary pancreatic stellate cells (PSC) treated with 8 tumor cell lines, 24h

description: Gene expression data _post treatment

data_processing: The data were processed with R using RMA normalization procedure (justRMA package), annotated with the corresponding library (hgu133plus2.db), and extracted in both unfiltered (normalized, complete set), and filtered (IQR filtering 0.25).

source_name: primary PSC

growth_protocol: regular growth in 10 cm Petri dishes at 37oC to 70% confluence

treatment_protocol: Tumor-cell supernatant was added 24, 7,6,5,4,3,2, and 1 prior harvest

tag: primary cells

value: PSC (Primary pancreatic stellate cells)


title: Tumor cells (MiaPaCa2) treated with naive stellate cells (PSC), 2h

description: MiaPaca2 post naive PSC-treatment


title: Whole right lung day 28 post-left pneumonectomy

value: day 28 post-left pneumonectomy


title: Right lung cardiac lobe day 56 post-left pneumonectomy

source_name: cardiac lobe of right lung

value: Right lung cardiac lobe


title: Primary pancreatic stellate cells (PSC) treated with 8 tumor cell lines, control 24h

description: Gene expression data _control


title: Primary pancreatic stellate cells (PSC) treated with 8 tumor cell lines, 7h

description: Gene expression data _post treatment


title: Tumor cells (MiaPaCa2) treated with naive stellate cells (PSC), 3h

description: MiaPaca2 post naive PSC-treatment


title: Right lung cardiac lobe day 7 post-left pneumonectomy


title: Right lung cardiac lobe day 28 post-left pneumonectomy


title: Right lung cardiac lobe day 0 pre-left pneumonectomy


title: Primary pancreatic stellate cells (PSC) treated with 8 tumor cell lines, 6h

description: Gene expression data _post treatment


title: Right lung cardiac lobe day 56 post sham surgery


title: Primary pancreatic stellate cells (PSC) treated with 8 tumor cell lines, 3h

description: Gene expression data _post treatment


title: Whole right lung day 3 post-left pneumonectomy

value: day 3 post-left pneumonectomy


title: Primary pancreatic stellate cells (PSC) treated with 8 tumor cell lines, 5h

description: Gene expression data _post treatment


title: Right lung cardiac lobe day 14 post-left pneumonectomy


title: Primary pancreatic stellate cells (PSC) treated with 8 tumor cell lines, 4h

description: Gene expression data _post treatment


title: RMh-9 (PBMC-infected)

city: Atlanta

first: Siddappa

last: Byrareddy

address: 101 Woodruff circle

department: Pathology & Laboratory Medicine

institute: Emory Univeristy

hyb_protocol: Hybridization and post-hybridization processing were performed following the Affymetrix GeneChip Expression Analysis standard protocols (Affymetrix inc.)

scan_protocol: The gene chips were scanned on Affymetrix scanner 3000

data_processing:
The data from gene chips was processed with GeneChip Operating Software (GCOS) 1.4
CEL files were processed and normalized using the robust multiarray average (RMA) algorithm. To identify genes correlating with the phenotypic groups, the data were fitted to a linear model using the limma package and tested for differential gene expression Genes with statistically significant differences between the naive vs. Rev-Ind Nef¯SIV infected were determined using a false-discovery-rate cutoff of <5% and a log fold-change cutoff of >1.  Expression values of significant probe sets were loaded into the MultiExperiment Viewer (MeV) and analyzed using average-linkage hierarchical clustering with a Pearson correlation coefficient distance metric.
Affymetrix CEL files were processed and normalized using the robust multiarray average (RMA) algorithm.  Principal component analysis (PCA) was performed on the normalized expression values to identify phenotypically similar groups by visualizing the top three principal components. To identify genes correlating with the phenotypic groups, the data were fitted to a linear model using the limma package and tested for differential gene expression.

organism: Macaca mulatta

label_protocol: Biotinylated complementary RNAs (cRNAs) were synthesized in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix by in vitro transcription (IVT) reaction.

extract_protocol: RNA was extracted with Rneasy mini kit (Qiagen)

treatment_protocol: Rhesus macaques were infected intravenously with Rev-Ind Nef¯SIV. The naïve rhesus PBMC were obtained from same animals before infection

tag: cell type

value: PBMC

tag: infection status

value: 2-weeks post nfected Rev-Ind Nef¯SIV infected Rhesus macaque PBMCs


title: RAm-5(PBMC-naive)

source_name: Naïve Rhesus macaque PBMCs

value: Naïve Rhesus macaque PBMCs


title: Primary pancreatic stellate cells (PSC) treated with 8 tumor cell lines, 2h

description: Gene expression data _post treatment


title: RRu-7 (PBMC-infected)

source_name: Rev-Ind Nef¯SIV infected Rhesus macaque PBMCs


title: RRu-7 (PBMC-naive)


title: Right lung medial lobe day 56 post-left pneumonectomy

source_name: medial lobe of right lung

value: Male

value: Right lung medial lobe


title: Right lung medial lobe day 7 post-left pneumonectomy

value: microarray hybridization data 06/06/2011


title: Right lung medial lobe day 56 post sham surgery

value: Sham surgery

value: day 56 post sham surgery


title: Right lung cardiac lobe day 3 post-left pneumonectomy

value: Left pneumonectomy


title: Right lung medial lobe day 14 post-left pneumonectomy

value: day 14 post-left pneumonectomy


title: RAm-5(PBMC-infected)


title: RMh-9 (PBMC-naive)

source_name: Naive Rhesus macaque PBMCs


title: Right lung medial lobe day 28 post-left pneumonectomy


title: Right lung medial lobe day 3 post-left pneumonectomy


title: Gsvcv_2

status: Public on Aug 08 2013

city: Elche

first: Amparo

last: Estepa Perez

state: Alicante

address: Av. Ferrocarril s/n

department: Institute of Molecular and Cell Biology

country: Spain

institute: University Miguel Hernandez

description: Gene expression in muscle samples of fish injected with the plasmid containing the gene sequence of the gpG of SVCV (experiment 2)

hyb_protocol: Each amplified and labelled sample was hybridized at 65 oC for 17 hours.

scan_protocol: Arrays were scanned and one-channel TIFF (FEATURE EXTRACTION software v. 10.4.0.0.) images were imported into GENESPRING software (GX v. 11.0)

data_processing: Data was analysed using GENESPRING software (GX v. 11.0.).Signal intensities for unique probes within a probe set were averaged to obtain an expression value (median) for the probe set (Gene-level analysis). expressed was defined as transcripts with a log2-transformed expression value greater than 1.

organism: Danio rerio

source_name: muscle (injection site)

label_protocol: Labelling of the samples with Cy3 according to manufacturer instructions (Agilent Technologies).

extract_protocol: RNA was isolated using the E.Z.N.A HP Tissue RNA kit (Omega bio-tek) according to intructions provided in the kit. RNA was kept at -80 oC until used.

treatment_protocol: Fish (n=4) were intramuscularly injected with 1,5 µg of the plasmid constructs containing the gene sequences of SVCV or VHSV glycoproteins or the empty plasmid. After three days muscle samples were excised from the site of injection and processed from RNA isolation and gene expression analysis with microarrays.

tag: age

value: adult (+ 6months)

value: muscle


title: Right lung medial lobe day 0 pre-left pneumonectomy

value: No pneumonectomy

value: day 0 pre-left pneumonectomy


title: Gvhsv_1

description: Gene expression in muscle samples of fish injected with the plasmid containing the gene sequence of the gpG of VHSV (experiment 1)


title: EP_1

description: Gene expression in muscle samples of fish injected with the empty plasmid (experiment 1)

value: fish injected with the empty plasmid


title: EP_3

description: Gene expression in muscle samples of fish injected with the empty plasmid (experiment 3)


title: EP_2

description: Gene expression in muscle samples of fish injected with the empty plasmid (experiment 2)


title: Gvhsv_2

description: Gene expression in muscle samples of fish injected with the plasmid containing the gene sequence of the gpG of VHSV (experiment 2)


title: Control_1

description: Gene expression in muscle samples of control fish (experiment 1)

value: control fish


title: Gsvcv_3

description: Gene expression in muscle samples of fish injected with the plasmid containing the gene sequence of the gpG of SVCV (experiment 3)


title: Control_2

description: Gene expression in muscle samples of control fish (experiment 2)


title: Control_3

description: Gene expression in muscle samples of control fish (experiment 3)


title: Primary pancreatic stellate cells (PSC) treated with 8 tumor cell lines, 1h

description: Gene expression data _post treatment

value: PSC (Primary pancreatic stellate cells)


title: Gvhsv_3

description: Gene expression in muscle samples of fish injected with the plasmid containing the gene sequence of the gpG of VHSV (experiment 3)


title: Gsvcv_1

description: Gene expression in muscle samples of fish injected with the plasmid containing the gene sequence of the gpG of SVCV (experiment 1)


title: CD cells_salt stressed_Bdkrb2 KO_rep2

city: NEW ORLEANS

first: Lei

last: Yan

state: LA

address: 1430 Tulane Ave #SL37

department: Pediatrics

institute: Tulane University

hyb_protocol: Hybridization was performed following Agilent’s oligonucleotide microarray hybridization User’s Manual and Agilent’s in situ Hybridization Plus kit. The labeled cDNA was hybridized to Agilent-015347 Regeneron Custom Whole Genome Oligo - mouse v1.0

scan_protocol: The arrays were scanned using a dual-laser DNA microarray scanner (Agilent).

data_processing: The data was then extracted from images by the Feature Extraction software 6.1 (Agilent). Lowess normalization was applied to correct for artifacts caused by non-linear rates of dye incorporation, as well as inconsistencies in the relative fluorescence intensity between some red and green dyes.

source_name: BdkrB2 KO New Born CD cells

label_protocol: The quality of RNA samples was assessed by capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Fluorescently labeled cDNA was generated from 0.5 μg of total RNA in each reaction using the Agilent Fluorescent Direct Label Kit and 1.0 mM Cyanine 3- or 5- labeled dCTP (PerkinElmer, Boston, MA), and following the User’s Manual.

growth_protocol: Hoxb7cre+; Bdkrb2 F/F; tdTomato mice on high salt food feeding were paired to Bdkrb2 F/F; tdTomato mice mice. Total RNA was isolated from GFP and dsRED positive collect cells FACS sorted from salt‐stressed Day 1 new born Hoxb7cre+; Bdkrb2f/f; R26RtdTomato and Hoxb7cre+; R26RtdTomato; Bdkrb2+/+kidneys.

extract_protocol: Total RNA extracted with Rneasy Mini kit according to manufacturer's protocol.

treatment_protocol: All experimental animals were put on 5% Sodium high salt food feeding.

tag: gestational salt status

value: High salt

tag: genotype/variation

value: BdkrB2 KO

source_name: BdkrB2 WT New Born CD cells (WT1 reference)

value: BdkrB2 WT


title: CD cells_salt stressed_Bdkrb2 WT_rep2

source_name: BdkrB2 WT New Born CD cells


title: CD cells_salt stressed_Bdkrb2 KO_rep3


title: myotubes_four and a half LIM domains 1 deficiency 2

city: Berlin

first: Anna

middle: Maria

last: Pakula

address: Lindenberger Weg 80

department: Experimental and Clinical Research Center (ECRC),Max-Delbrück-Centrum feur Molekulare Medizin (MDC) Berlin, Institut de Myologie NMR-Spectroscopy Laboratory Université Pierre et Marie Curie, Paris 6

institute: Charite University Berlin

description: myotubes

hyb_protocol: samples were hybridized at 45 (°C) and 60rpm for 17+/- 1h to the GeneChip Human Exon 1.0 ST ARRAY (Affymetrix) in a GeneChip Hybridization Oven 640 (Affymetrix) tham wash and stained on a GeneChip Fluidics Station 450 system.

scan_protocol: Affymetrix GeneArray scanner 3000 7G

data_processing:
Probes of the full meta-probe-set normalized, after pre-background adjustment for GC contend, using Partek Genomic Suite 6.3, RMA background correction, quantile normalization and mean probeset summarization
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

source_name: Vastus lateralis

label_protocol: 5 µg of cDNA was labeled using terminal deoxynucleotidyl tranferase (TdT)samples in the presence of a proprietary biotinylated compound by use of gene Chip WT Terminal Labelling Kit, Affymetrix

growth_protocol: Primary myoblast cultures were isolated from fresh muscle biopsies from  patients and healthy control subjects as previously described (Philippi et al. 2012).

extract_protocol: Total RNA was isolated from 22 Myotubes cultures ( derived from human muscle biopsies) by using standard Trizol reagent (Invitrogen Darmstadt,Germany).Total RNA was treated by deoxyribonuclease I (RNAse-Free DNAse set, Ambion, Darmstadt germant) and purified using an RNAeasy Purification Kit (Qiagen, Hilden, Germany).Samples of 250ng of RNA were transcribed using WT Expression Kit (Ambion, Austin, TX, USA).

treatment_protocol: not applicable

tag: disease state

tag: age (years)

value: myotubes


title: CD cells_salt stressed_Bdkrb2 WT_rep3


title: Chironomus riparius_high conc_phenanthrene_replicate 9

city: Amsterdam

first: Floyd

last: Wittink

address: Kruislaan 318

department: MAD

country: Netherlands

institute: Universiteit van Amsterdam

description: Chironomus riparius high conc. phenanthrene treated sample replicate 9

hyb_protocol: Hybridization samples, containing 1.1 µg test (Cy3) and 1.1 µg common reference (Cy5) sample, were made according to the manufacturer's instructions (NimbleGen Arrays User's Guide for Gene Expression Arrays Version 5.0, Roche/NimbleGen). Hybridization of the samples to the custom made 12*135K C. riparius microarrays (Marinković et al., 2012) was carried out for 18 hours at 42°C using NimbleGen Hybridization System 4 (Roche/Nimblegen).

scan_protocol: Microarrays were scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies).

data_processing: Feature extraction was performed with NimbleScan v2.5 (Roche/Nimblegen). The data was normalized using the vsn algorithm that performs intensity-based variance stabilization (Huber et al., 2002) and the duplicate probes per transcript were collapsed.

organism: Chironomus riparius

source_name: high conc. phenanthrene

label_protocol: Per sample, 500 ng total RNA was amplified according to the Agilent QuickAmp kit manual (Agilent technologies).  Amino-allyl modified nucleotides were incorporated during the aRNA synthesis (2.5 mM rGAU (GE Healthcare), 0.75 mM  rCTP (GE Healthcare), 0.75 mM AA-rCTP (TriLink Biotechnologies).  Synthesized aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit (Omega Bio-Tek). Test samples were labeled with Cy3 and a Common Reference sample (made by pooling equimolar amounts of RNA from Test samples) was labeled with Cy5.  5 µg of aRNA was dried down and dissolved in 50 mM carbonate buffer pH 8.5. Individual vials of Cy3/Cy5 from the mono-reactive dye packs (GE Healthcare) were dissolved in 200 µl DMSO. To each sample, 10 µl of the appropriate CyDye dissolved in DMSO was added and the mixture was incubated for 1h. Reactions were quenched with the addition of 5 µl 4M hydroxylamine (Sigma-Aldrich). The labeled aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit. The yields of aRNA and CyDye incorporation were measured on the NanoDrop ND-1000.

growth_protocol: The experiments were conducted with the University of Amsterdam’s Chironomus riparius culture that was maintained in aquaria containing quartz sand overlaid with Dutch Standard Water at 20 ± 1 ˚C, 65% humidity and a 16: 8 h light: dark photoperiod (Marinković et al., 2011). The culture was fed a mixture of Trouvit® (Trouw, Fontaine-les-Vervins, France) and Tetraphyll® (Tetrawerke, Melle, Germany) in a weight ratio of 20:1. This mixture was also used as food for all subsequent experiments.

extract_protocol: RNA was isolated from individual flash frozen C. riparius larvae using Qiazol (Qiagen) for RNA extraction and RNeasy MinElute columns (Qiagen) for RNA purification. RNA yield was determined on a NanoDrop ND-1000 UV-VIS spectrophotometer (Thermo Fisher Scientific), while RNA integrity was examined using a RNA 6000 Nano chip on a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: The 14-day Chironomus riparius sediment toxicity tests were conducted based on OECD guideline 218 (OECD, 2004) with slight modifications. OECD. Chironomid toxicity test using spiked sediment; Guideline for Testing of Chemicals No. 218; Organisation for Economic Co-operation and Development: Paris, 2004.

value: larvae


title: CD cells_salt stressed_Bdkrb2 WT_rep1


title: CD cells_salt stressed_Bdkrb2 KO_rep1


title: Chironomus riparius_high conc_phenanthrene_replicate 10

description: Chironomus riparius high conc. phenanthrene treated sample replicate 10


title: myotubes_facioscapulohumeral dystrophy 4

description: myotubes

value: facioscapulohumeral dystrophy


title: myotubes_caveolinopathy 3 3

description: myotubes

value: caveolinopathy 3


title: myotubes_four and a half LIM domains 1 deficiency 3

description: myotubes


title: myotubes_caveolinopathy 3 4

description: myotubes


title: Chironomus riparius_high conc_phenanthrene_replicate 4

description: Chironomus riparius high conc. phenanthrene treated sample replicate 4


title: Chironomus riparius_high conc_phenanthrene_replicate 8

description: Chironomus riparius high conc. phenanthrene treated sample replicate 8


title: Chironomus riparius_high conc_phenanthrene_replicate 5

description: Chironomus riparius high conc. phenanthrene treated sample replicate 5


title: Chironomus riparius_high conc_phenanthrene_replicate 6

description: Chironomus riparius high conc. phenanthrene treated sample replicate 6


title: Chironomus riparius_high conc_phenanthrene_replicate 2

description: Chironomus riparius high conc. phenanthrene treated sample replicate 2


title: Chironomus riparius_moderate conc_phenanthrene_replicate 10

description: Chironomus riparius moderate conc. phenanthrene treated sample replicate 10

source_name: moderate conc. phenanthrene


title: myotubes_facioscapulohumeral dystrophy 1

description: myotubes


title: myotubes_facioscapulohumeral dystrophy 3

description: myotubes


title: Chironomus riparius_high conc_phenanthrene_replicate 1

description: Chironomus riparius high conc. phenanthrene treated sample replicate 1


title: Chironomus riparius_high conc_phenanthrene_replicate 7

description: Chironomus riparius high conc. phenanthrene treated sample replicate 7


title: myotubes_healthy control 7

description: myotubes

value: healthy control


title: myotubes_dysferlinopathy 3

description: myotubes

value: dysferlinopathy


title: myotubes_healthy control 6

description: myotubes


title: myotubes_facioscapulohumeral dystrophy 2

description: myotubes


title: myotubes_healthy control 5

description: myotubes


title: myotubes_caveolinopathy 3 1

description: myotubes


title: myotubes_four and a half LIM domains 1 deficiency 1

description: myotubes


title: myotubes_dysferlinopathy 2

description: myotubes


title: myotubes_dysferlinopathy 1

description: myotubes


title: myotubes_healthy control 3

description: myotubes


title: myotubes_healthy control 4

description: myotubes


title: Chironomus riparius_moderate conc_phenanthrene_replicate 8

description: Chironomus riparius moderate conc. phenanthrene treated sample replicate 8


title: myotubes_healthy control 1

description: myotubes


title: Chironomus riparius_moderate conc_phenanthrene_replicate 5

description: Chironomus riparius moderate conc. phenanthrene treated sample replicate 5


title: Chironomus riparius_moderate conc_phenanthrene_replicate 7

description: Chironomus riparius moderate conc. phenanthrene treated sample replicate 7


title: Chironomus riparius_moderate conc_phenanthrene_replicate 4

description: Chironomus riparius moderate conc. phenanthrene treated sample replicate 4


title: Chironomus riparius_moderate conc_phenanthrene_replicate 6

description: Chironomus riparius moderate conc. phenanthrene treated sample replicate 6


title: myotubes_healthy control 2

description: myotubes


title: Chironomus riparius_moderate conc_phenanthrene_replicate 2

description: Chironomus riparius moderate conc. phenanthrene treated sample replicate 2


title: myotubes_dysferlinopathy 4

description: myotubes


title: Chironomus riparius_moderate conc_phenanthrene_replicate 3

description: Chironomus riparius moderate conc. phenanthrene treated sample replicate 3


title: Chironomus riparius_moderate conc_phenanthrene_replicate 9

description: Chironomus riparius moderate conc. phenanthrene treated sample replicate 9


title: Chironomus riparius_moderate conc_phenanthrene_replicate 1

description: Chironomus riparius moderate conc. phenanthrene treated sample replicate 1


title: Chironomus riparius_low conc_phenanthrene_replicate 8

description: Chironomus riparius low  conc. phenanthrene treated sample replicate 8

source_name: low conc. phenanthrene


title: Chironomus riparius_low conc_phenanthrene_replicate 9

description: Chironomus riparius low  conc. phenanthrene treated sample replicate 9


title: Chironomus riparius_low conc_phenanthrene_replicate 7

description: Chironomus riparius low  conc. phenanthrene treated sample replicate 7


title: Chironomus riparius_low conc_phenanthrene_replicate 10

description: Chironomus riparius low  conc. phenanthrene treated sample replicate 10


title: Chironomus riparius_low conc_phenanthrene_replicate 6

description: Chironomus riparius low  conc. phenanthrene treated sample replicate 6


title: Chironomus riparius_low conc_phenanthrene_replicate 5

description: Chironomus riparius low  conc. phenanthrene treated sample replicate 5


title: myotubes_caveolinopathy 3 2

description: myotubes


title: Chironomus riparius_low conc_phenanthrene_replicate 1

description: Chironomus riparius low  conc. phenanthrene treated sample replicate 1


title: Chironomus riparius_high conc_phenanthrene_replicate 3

description: Chironomus riparius high conc. phenanthrene treated sample replicate 3


title: Chironomus riparius_high conc_tributyltin_replicate 7

description: Chironomus riparius high conc.  tributyltin treated sample replicate 7

source_name: high conc. tributyltin


title: Chironomus riparius_low conc_phenanthrene_replicate 3

description: Chironomus riparius low  conc. phenanthrene treated sample replicate 3


title: Chironomus riparius_low conc_phenanthrene_replicate 2

description: Chironomus riparius low  conc. phenanthrene treated sample replicate 2


title: Chironomus riparius_high conc_tributyltin_replicate 9

description: Chironomus riparius high conc.  tributyltin treated sample replicate 9


title: Chironomus riparius_low conc_phenanthrene_replicate 4

description: Chironomus riparius low  conc. phenanthrene treated sample replicate 4


title: Chironomus riparius_high conc_tributyltin_replicate 8

description: Chironomus riparius high conc.  tributyltin treated sample replicate 8


title: Chironomus riparius_high conc_tributyltin_replicate 4

description: Chironomus riparius high conc.  tributyltin treated sample replicate 4


title: Chironomus riparius_high conc_tributyltin_replicate 1

description: Chironomus riparius high conc.  tributyltin treated sample replicate 1


title: Chironomus riparius_moderate conc_tributyltin_replicate 9

description: Chironomus riparius moderate conc. tributyltin treated sample replicate 9

source_name: moderate conc. tributyltin


title: Chironomus riparius_moderate conc_tributyltin_replicate 4

description: Chironomus riparius moderate conc. tributyltin treated sample replicate 4


title: Chironomus riparius_high conc_tributyltin_replicate 10

description: Chironomus riparius high conc.  tributyltin treated sample replicate 10


title: Chironomus riparius_moderate conc_tributyltin_replicate 8

description: Chironomus riparius moderate conc. tributyltin treated sample replicate 8


title: Chironomus riparius_low conc_tributyltin_replicate 10

description: Chironomus riparius low  conc. tributyltin treated sample replicate 10

source_name: low conc. tributyltin


title: Chironomus riparius_moderate conc_tributyltin_replicate 10

description: Chironomus riparius moderate conc. tributyltin treated sample replicate 10


title: Chironomus riparius_moderate conc_tributyltin_replicate 7

description: Chironomus riparius moderate conc. tributyltin treated sample replicate 7


title: Chironomus riparius_moderate conc_tributyltin_replicate 2

description: Chironomus riparius moderate conc. tributyltin treated sample replicate 2


title: Chironomus riparius_moderate conc_tributyltin_replicate 6

description: Chironomus riparius moderate conc. tributyltin treated sample replicate 6


title: Chironomus riparius_high conc_tributyltin_replicate 6

description: Chironomus riparius high conc.  tributyltin treated sample replicate 6


title: Chironomus riparius_low conc_tributyltin_replicate 8

description: Chironomus riparius low  conc. tributyltin treated sample replicate 8


title: Chironomus riparius_high conc_tributyltin_replicate 3

description: Chironomus riparius high conc.  tributyltin treated sample replicate 3


title: Chironomus riparius_moderate conc_tributyltin_replicate 5

description: Chironomus riparius moderate conc. tributyltin treated sample replicate 5


title: Chironomus riparius_low conc_tributyltin_replicate 3

description: Chironomus riparius low  conc. tributyltin treated sample replicate 3


title: Chironomus riparius_moderate conc_tributyltin_replicate 3

description: Chironomus riparius moderate conc. tributyltin treated sample replicate 3


title: Chironomus riparius_moderate conc_tributyltin_replicate 1

description: Chironomus riparius moderate conc. tributyltin treated sample replicate 1


title: Chironomus riparius_low conc_tributyltin_replicate 4

description: Chironomus riparius low  conc. tributyltin treated sample replicate 4


title: Chironomus riparius_low conc_tributyltin_replicate 9

description: Chironomus riparius low  conc. tributyltin treated sample replicate 9


title: Chironomus riparius_low conc_tributyltin_replicate 6

description: Chironomus riparius low  conc. tributyltin treated sample replicate 6


title: Chironomus riparius_low conc_tributyltin_replicate 7

description: Chironomus riparius low  conc. tributyltin treated sample replicate 7


title: Chironomus riparius_low conc_tributyltin_replicate 2

description: Chironomus riparius low  conc. tributyltin treated sample replicate 2


title: Chironomus riparius_low conc_tributyltin_replicate 1

description: Chironomus riparius low  conc. tributyltin treated sample replicate 1


title: Chironomus riparius_low conc_tributyltin_replicate 5

description: Chironomus riparius low  conc. tributyltin treated sample replicate 5


title: Chironomus riparius_high conc_tributyltin_replicate 5

description: Chironomus riparius high conc.  tributyltin treated sample replicate 5


title: Chironomus riparius_high conc_copper_replicate 10

description: Chironomus riparius high conc.  copper treated sample replicate 10

source_name: high conc. copper


title: Lung-d49_SeV-3b

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

description:
Strip B from array and sample B6.49.S.3745 each BeadChip consists of two strips (A & B).
B6.49.S.3745.2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol except for adding output of raw array data for beadlevel analyses

data_processing: Hybridization and scanning of BeadChip arrays was performed according to the manufacturer’s instructions, using BeadStudio 3.0 software (Illumina). In order to perform bead-level analysis, raw data is exported from BeadStudio. Microarray normalization and statistical analysis was performed using packages from the Bioconductor project executed in the R programming environment. Raw bead-level intensity data was imported using functions from the beadarray package, including background correction. Each Mouse-WG6 v2 BeadChip array consists of two strips. Due to potential variation in the data from the two different strips (see Shi et al. (2009) [PMID:19903361]), we treated the individual strips from each sample separately through bead-summarization. Thus, for each strip, low-level analysis and quality control was performed using functions from the beadarray package (see Ritchie et al. (2011) [PMID:22144879]). The BASH algorithm was then applied to the raw data to mask beads affected by large spatial artifacts, followed by bead-type summarization, including removal of outlier beads. Summarized data were Log2-transformed, followed by quantile normalization.

source_name: whole lung, SeV post-infection day 49, rep 3, array strip B

label_protocol: Biotinylated aRNA were prepared using the Illumina TotalPrep Kit (Ambion) per manufacturer's protocol.

growth_protocol: Mice were maintained under pathogen-free conditions, and all study protocols were approved by the Washington University Animal Studies Committee.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy kit per manufacturer's protocol. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Sendai virus (SeV), strain 52, was obtained from American Type Culture Collection and stored at -70°C. Mice were inoculated with SeV or an equivalent amount of UV-inactivated SeV (SeV-UV) intranasally. 3-5 week old male C57BL/6J mice were obtained from Jackson Laboratory. Mice were sacrificed post-infection day 49, and lungs were harvested, right for RNA, left for histology and other studies (see Kim et al, 2008, PMID:18488036).

value: 49 days post-infection

tag: infection

value: active Sendai virus

tag: gender

value: Male


title: Chironomus riparius_high conc_copper_replicate 6

description: Chironomus riparius high conc.  copper treated sample replicate 6


title: Chironomus riparius_high conc_copper_replicate 7

description: Chironomus riparius high conc.  copper treated sample replicate 7


title: Chironomus riparius_high conc_copper_replicate 9

description: Chironomus riparius high conc.  copper treated sample replicate 9


title: Chironomus riparius_high conc_copper_replicate 5

description: Chironomus riparius high conc.  copper treated sample replicate 5


title: Chironomus riparius_high conc_copper_replicate 4

description: Chironomus riparius high conc.  copper treated sample replicate 4


title: Chironomus riparius_moderate conc_copper_replicate 9

description: Chironomus riparius moderate conc. copper treated sample replicate 9

source_name: moderate conc. copper


title: Chironomus riparius_high conc_copper_replicate 8

description: Chironomus riparius high conc.  copper treated sample replicate 8


title: Lung-d49_UVSeV-3b

description:
Strip B from array and sample B6.49.U.3735 each BeadChip consists of two strips (A & B).
B6.49.U.3735.2

source_name: whole lung, UV-SeV post-infection day 49, rep 3, array strip B

value: UV-inactivated Sendai virus


title: Chironomus riparius_high conc_copper_replicate 2

description: Chironomus riparius high conc.  copper treated sample replicate 2


title: Chironomus riparius_moderate conc_copper_replicate 7

description: Chironomus riparius moderate conc. copper treated sample replicate 7


title: Chironomus riparius_high conc_copper_replicate 1

description: Chironomus riparius high conc.  copper treated sample replicate 1


title: Lung-d49_SeV-3a

description:
Strip A from array and sample B6.49.S.3745 each BeadChip consists of two strips (A & B).
B6.49.S.3745.1

source_name: whole lung, SeV post-infection day 49, rep 3, array strip A


title: Chironomus riparius_moderate conc_copper_replicate 6

description: Chironomus riparius moderate conc. copper treated sample replicate 6


title: Lung-d49_SeV-2b

description:
Strip B from array and sample B6.49.S.3744 each BeadChip consists of two strips (A & B).
B6.49.S.3744.2

source_name: whole lung, SeV post-infection day 49, rep 2, array strip B


title: Chironomus riparius_high conc_copper_replicate 3

description: Chironomus riparius high conc.  copper treated sample replicate 3


title: Lung-d49_SeV-1a

description:
Strip A from array and sample B6.49.S.3743 each BeadChip consists of two strips (A & B).
B6.49.S.3743.1

source_name: whole lung, SeV post-infection day 49, rep 1, array strip A


title: Lung-d49_UVSeV-2a

description:
Strip A from array and sample B6.49.U.3736 each BeadChip consists of two strips (A & B).
B6.49.U.3736.1

source_name: whole lung, UV-SeV post-infection day 49, rep 2, array strip A


title: Chironomus riparius_moderate conc_copper_replicate 5

description: Chironomus riparius moderate conc. copper treated sample replicate 5


title: Lung-d49_UVSeV-2b

description:
Strip B from array and sample B6.49.U.3736 each BeadChip consists of two strips (A & B).
B6.49.U.3736.2

source_name: whole lung, UV-SeV post-infection day 49, rep 2, array strip B


title: Lung-d49_SeV-1b

description:
Strip B from array and sample B6.49.S.3743 each BeadChip consists of two strips (A & B).
B6.49.S.3743.2

source_name: whole lung, SeV post-infection day 49, rep 1, array strip B


title: Chironomus riparius_moderate conc_copper_replicate 10

description: Chironomus riparius moderate conc. copper treated sample replicate 10


title: Lung-d49_SeV-2a

description:
Strip A from array and sample B6.49.S.3744 each BeadChip consists of two strips (A & B).
B6.49.S.3744.1

source_name: whole lung, SeV post-infection day 49, rep 2, array strip A


title: Lung-d49_UVSeV-3a

description:
Strip A from array and sample B6.49.U.3735 each BeadChip consists of two strips (A & B).
B6.49.U.3735.1

source_name: whole lung, UV-SeV post-infection day 49, rep 3, array strip A


title: Lung-d49_UVSeV-1b

description:
Strip B from array and sample B6.49.U.3734 each BeadChip consists of two strips (A & B).
B6.49.U.3734.2

source_name: whole lung, UV-SeV post-infection day 49, rep 1, array strip B


title: Lung-d49_UVSeV-1a

description:
Strip A from array and sample B6.49.U.3734 each BeadChip consists of two strips (A & B).
B6.49.U.3734.1

source_name: whole lung, UV-SeV post-infection day 49, rep 1, array strip A


title: Chironomus riparius_moderate conc_copper_replicate 2

description: Chironomus riparius moderate conc. copper treated sample replicate 2


title: Chironomus riparius_low conc_copper_replicate 10

description: Chironomus riparius low  conc. copper treated sample replicate 10

source_name: low conc. copper


title: HUVEC cells from umbilical cords of gestational diabetic mothers GD3

city: Rome

first: Guido

last: Leoni

address: Via Pontina

department: Bioinformatics

country: Italy

institute: IRBM

description: Gene expression data from gestational diabetes samples

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on custom Affymetrix chips (NuGO_Hs1a520180). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were normalized with the GCRMA algorithm and analyzed with oneChannelGUI package included in R software

source_name: GESTATIONAL DIABETES

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

value: female

tag: ethnicity

value: Caucasian

tag: condition

value: gestational diabetes

value: umbilical cord

value: primary endothelial cells from umbilical cord vein (HUVEC)


title: Chironomus riparius_moderate conc_copper_replicate 4

description: Chironomus riparius moderate conc. copper treated sample replicate 4


title: Chironomus riparius_moderate conc_copper_replicate 8

description: Chironomus riparius moderate conc. copper treated sample replicate 8


title: HUVEC cells from umbilical cord of controls C2

description: Gene expression data from controls

source_name: CONTROL

value: control


title: HUVEC cells from umbilical cord of controls C1

description: Gene expression data from controls


title: Chironomus riparius_high conc_cadmium_replicate 9

description: Chironomus riparius high conc.  cadmium treated sample replicate 9

source_name: high conc. cadmium


title: Chironomus riparius_moderate conc_copper_replicate 3

description: Chironomus riparius moderate conc. copper treated sample replicate 3


title: slide180837

city: Groningen

first: Jetta

last: Bijlsma

address: Hanzeplein 1

department: Medical Microbiology

institute: University Medical Center Groningen

description: Sample 2

hyb_protocol: The protocol was performed as described in Hendriksen et al., 2008 (PMID: 18024519)

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (15, 18, 49). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Streptococcus pneumoniae D39

source_name: Net {A}

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences

growth_protocol: Cells were grown to OD600 of 0.25 in GM17 media

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Hendriksen et al., 2007; Hendriksen et al., 2008a). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

value: spxB

source_name: Net {B}


title: HUVEC cells from umbilical cords of gestational diabetic mothers GD1


title: Chironomus riparius_low conc_copper_replicate 9

description: Chironomus riparius low  conc. copper treated sample replicate 9


title: slide180838

description: Sample 3


title: HUVEC cells from umbilical cord of controls C3

description: Gene expression data from controls


title: slide180839

description: Sample 4


title: Chironomus riparius_high conc_cadmium_replicate 10

description: Chironomus riparius high conc.  cadmium treated sample replicate 10


title: Chironomus riparius_low conc_copper_replicate 5

description: Chironomus riparius low  conc. copper treated sample replicate 5


title: Chironomus riparius_low conc_copper_replicate 8

description: Chironomus riparius low  conc. copper treated sample replicate 8


title: Chironomus riparius_low conc_copper_replicate 6

description: Chironomus riparius low  conc. copper treated sample replicate 6


title: Chironomus riparius_low conc_copper_replicate 4

description: Chironomus riparius low  conc. copper treated sample replicate 4


title: Chironomus riparius_low conc_copper_replicate 3

description: Chironomus riparius low  conc. copper treated sample replicate 3


title: Chironomus riparius_low conc_copper_replicate 1

description: Chironomus riparius low  conc. copper treated sample replicate 1


title: Chironomus riparius_moderate conc_copper_replicate 1

description: Chironomus riparius moderate conc. copper treated sample replicate 1

source_name: moderate conc. copper


title: Chironomus riparius_high conc_cadmium_replicate 8

description: Chironomus riparius high conc.  cadmium treated sample replicate 8


title: slide180836

description: Sample 1


title: Chironomus riparius_low conc_copper_replicate 2

description: Chironomus riparius low  conc. copper treated sample replicate 2


title: HUVEC cells from umbilical cords of gestational diabetic mothers GD2


title: Chironomus riparius_high conc_cadmium_replicate 7

description: Chironomus riparius high conc.  cadmium treated sample replicate 7


title: Chironomus riparius_high conc_cadmium_replicate 6

description: Chironomus riparius high conc.  cadmium treated sample replicate 6


title: Chironomus riparius_high conc_cadmium_replicate 2

description: Chironomus riparius high conc.  cadmium treated sample replicate 2


title: Chironomus riparius_high conc_cadmium_replicate 4

description: Chironomus riparius high conc.  cadmium treated sample replicate 4


title: Chironomus riparius_high conc_cadmium_replicate 3

description: Chironomus riparius high conc.  cadmium treated sample replicate 3


title: Chironomus riparius_high conc_cadmium_replicate 5

description: Chironomus riparius high conc.  cadmium treated sample replicate 5


title: 26-B APE-10

city: Shanghai

first: junjie

last: xiao

address: 150 Ji Mo Road

country: China

institute: Key Laboratory of Arrhythmias, Ministry of Education, China (Tongji University School of Medicine)

description: Tagman-based qRT PCR

hyb_protocol: MiRNAs were reverse-transcribed using the Megaplex Primer Pools (Human Pools A v2.1 and B v2.0), and the products were preamplified according to the ABI preamplification protocol. MiRNAs expression was screened using Taqman miRNA microarrays A and B according to the manufacturer protocol (all from Applied Biosystems, Foster City, CA).

scan_protocol: MiRNAs expression was screened using Taqman miRNA microarrays A and B according to the manufacturer protocol (all from Applied Biosystems, Foster City, CA). All steps were performed using a 7900HT Fast Real-Time PCR System (Applied Biosystems, Foster City, CA).

data_processing: For the lack of generally accepted standards all qPCR data of single miRNAs expression were analyzed as unadjusted Ct values and standardized to miR-16 (A plate) or miR-135a*(B plate).

label: Tagman

source_name: Plasma

label_protocol: Tagman-based qRT PCR

extract_protocol: Total RNA was isolated from plasma using mirVana PARIS isolation kit (Ambion, Austin, Texas) according to the manufacturer’s instructions for plasma samples. Briefly, each of 400 μL human plasma was used to extract total RNA. Each sample was eluted in 100 μL of RNAsefree water.

value: male


title: 27-B Healthy control-10

description: Tagman-based qRT PCR


title: Chironomus riparius_moderate conc_cadmium_replicate 10

description: Chironomus riparius moderate conc.cadmium treated sample replicate 10

source_name: moderate conc. cadmium

value: larvae


title: cells 46 hours post dexamethasone shock, biological rep3

city: Irvine

first: Paolo

last: Sassone-Corsi

address: 340 Sprague Hall

department: Center for Epigenetics and Metabolism. Dept. Biological Chemistry

institute: University of California

description:
Sample name: CT46_3
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

hyb_protocol: 0.54 mg of single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix (GeneChip® Mouse Gene 1.0 ST) array. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007)

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files

data_processing: These probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP). (Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile)

source_name: Wild type mouse embryonic fibroblasts 46 hours post dexamethasone shock

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip® WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix GenechipÒ WT cDNA Amplification Kit. 10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation. The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChipÒ WT Sense Target Labeling Assay Manual). The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Cultured in DMEM supplemented with 5% NCS , 5% heat inactivated FBS and aminoacids

extract_protocol: Total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up. Eluted total RNAs were quantified (Nanodrop) with a portion of the recovered total RNA adjust to a final concentration of 100ng/ul.

treatment_protocol: Serum shock treated with 100 nM Dexamethasone (in DMEM) for 2h

value: wild type

value: 46 hours post dexamethasone shock

value: embryonic fibroblast


title: 25-B Healthy control-9

description: Tagman-based qRT PCR


title: 23-B Healthy control-7

description: Tagman-based qRT PCR


title: 24-B Healthy control-8

description: Tagman-based qRT PCR


title: Chironomus riparius_high conc_cadmium_replicate 1

description: Chironomus riparius high conc.  cadmium treated sample replicate 1


title: Dbp 4C Bmal1KO CT22

type: genomic

description:
Sample name:
data_418210_SLOT02_S01_Red/data_418210_SLOT02_S01_Green:BLOCK1
Background strain details: MEFs for our study were established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

hyb_protocol: 25-30 µg of the Cy5-labeled 4C DNA was mixed with an equal amount of Cy3-labeled genomic DNA and precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol. DNA was recovered and hybridized in 39ul hybridization buffer following chromatin immunoprecipitation (ChIP)-chip protocols (Nimblegen Systems; chapter 4 in http://www.nimblegen.com/products/lit/NG_ChIP-chip_Guide_v6p2.pdf). Arrays were sealed with Maui mixer SL and hybridized in Maui hybridization stations for 24 h at 42C. Arrays were washed at room temperature in 6X SSPE/5x10E-3 % Sodium N-lauroylsarcosinate for 5 minutes and two 5 minutes washes with 0.06% SSPE

scan_protocol: Arrays were scanned on an Agilent G2939A scanner following manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2 ChIP data extraction. LogRatios of PAIR file values were taken; then quantile normalization was applied. The normalization was performed using a custom-written code in the statistical programming language R.

molecule: genomic DNA

source_name: Control

label_protocol: 1 µg purified 4C DNA was labeled with Cy5. Genomic DNA from the corresponding cell cut with HindIII and Csp6I was similarly labeled with Cy3 as a control for hybridization efficiency. Labeling was done according to standard chromatin immunoprecipitation (ChIP)-chip protocols (Nimblegen Systems; chapter 3 in

extract_protocol: For each experiment, 20 million cells were synchronized with dexamethasone. Crosslinking was done in a final concentration of 2% formaldehyde, at 37ºC for 10 min. The reaction was quenched by the addition of glycine (final concentration 0.125 M). Cells were washed with cold PBS and lysed for 1 hour at 4 ºC with nuclear extraction buffer (10mM Tris-HCl, pH8.0, 10 mM NaCl, 0.2% NP-40, 1X complete protease inhibitors (Roche)). Cells were collected by centrifugation, resuspended in 1 ml of restriction buffer (New England Biolabs Buffer 2) and kept frozen at -80ºC until all samples were harvested and processed. Once all the samples were ready, a final concentration of 0.3% SDS was added to 10 million cells, and incubated at 37ºC during one hour. Triton X-100 was then added to a final concentration of 1.8%, and samples were incubated during 1 hour at 37 ºC. Crosslinked DNA was digested with 500 U of HindIII (New England Biolabs) at 37ºC overnight. The enzyme was heat inactivated (65ºC for 30 min) and the reaction was resuspended in a total volume of 7 ml with 1X ligation buffer and 100 U of T4 DNA Ligase (Roche), followed by incubation at 16ºC overnight. Samples were treated with 500 ug of Proteinase K (Ambion) and crosslinking was reversed at 65ºC overnight. DNA was phenol extracted and ethanol precipitated. 50 ug of this 3C template were digested overnight with 50 U of Csp6I enzyme (Fermentas). The enzyme was heat inactivated and the DNA was phenol extracted, ethanol precipitated and subsequently ligated at low concentration to promote circularization, that is, intramolecular ligation events, in a final volume of 7 ml with 100 U of T4 DNA Ligase (Roche). Ligation products were phenol extracted and ethanol precipitated using glycogen as a carrier.   PCR reactions were performed using the Expand Long Template PCR system (Roche). We used the maximum amount of template that still shows a linear amplification by testing serial dilutions of each sample and quantifying the PCR products in agarose gels, using QuantityOne software. Finally, PCRs were done in a PTC-100 thermal cycler (Bio-Rad) using the following conditions: 2 min at 95 °C, followed by 30 cycles of 15 s at 94 °C , 1 min at 60 ºC and 3 min at 68 ºC; and a final extension step of 7 min at 68 ºC was included. Dbp bait was amplified with the following inverse primers: Dbp4CHindIII: 5’-TCACAGGGTTTATGCCTGACAGGAT-3’; Dbp4CCsp6I: 5’-AGCACTGGTTTTTGCCTGGCGGTC-3’. 16 PCR reactions were pooled and purified using the QUIAquick nucleotide removal kit (Quiagen).

treatment_protocol: Dexamethasone for 2 hours. Wash. Harvest after 22 hours

value: Mouse embryonic fibroblast

tag: genotype

tag: sample type

value: input

source_name: Dbp 4C from Bmal1-/- MEFs at circadian time 22 post dexamethasone synchronization

tag: sample

value: Dbp 4C DNA


title: Dbp 4C WT CT46

description:
Sample name:
data_418206_WT5_46h_Rep1_Red_Cy5/data_418206_WT5_46h_Rep1_Green_Cy3:BLOCK1
Background strain details: MEFs for our study were established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

treatment_protocol: Dexamethasone for 2 hours. Wash. Harvest after 46 hours

value: Wild type

source_name: Dbp 4C from WT MEFs at circadian time 46 post dexamethasone synchronization


title: Chironomus riparius_moderate conc_cadmium_replicate 9

description: Chironomus riparius moderate conc.cadmium treated sample replicate 9

tag: tissue


title: Dbp 4C WT CT26

description:
Sample name:
data_411417_SLOT01_S01_Red/data_411417_SLOT01_S01_Green:BLOCK1
Background strain details: MEFs for our study were established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

treatment_protocol: Dexamethasone for 2 hours. Wash. Harvest after 26 hours

tag: time

source_name: Dbp 4C from WT MEFs at circadian time 26 post dexamethasone synchronization


title: 22-B Healthy control-6

description: Tagman-based qRT PCR


title: Chironomus riparius_moderate conc_cadmium_replicate 7

description: Chironomus riparius moderate conc.cadmium treated sample replicate 7


title: Chironomus riparius_moderate conc_cadmium_replicate 8

description: Chironomus riparius moderate conc.cadmium treated sample replicate 8


title: Dbp 4C Bmal1KO CT34

description:
Sample name:
data_418216_SLOT03_S01_Red/data_418216_SLOT03_S01_Green:BLOCK1
Background strain details: MEFs for our study were established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

treatment_protocol: Dexamethasone for 2 hours. Wash. Harvest after 34 hours

source_name: Dbp 4C from Bmal1-/- MEFs at circadian time 34 post dexamethasone synchronization


title: genomic DNA from liver sample 86

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

description: unknown

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio V2011.1; methylation module 1.9.0

label: Cy5 and Cy3

source_name: liver tissue 86

label_protocol: Standard Illumina Protocol

extract_protocol: For homogenisation of five to ten milligram frozen tissue and subsequent nucleic acid isolation, tubes with 1.4 mm ceramic beads (Precellys, Villeurbanne, France) and the AllPrep DNA/RNA Mini Kit (QIAGEN, Hilden, Germany) were used.

tag: group

value: unknown

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: bmi

value: liver


title: Dbp 4C WT CT34

description:
Sample name:
data_418204_WT4_34h_Rep1_Red_Cy5/data_418204_WT4_34h_Rep1_Green_Cy3:BLOCK1
Background strain details: MEFs for our study were established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

tag: cell type

source_name: Dbp 4C from WT MEFs at circadian time 34 post dexamethasone synchronization


title: Dbp 4C WT2 CT22

description:
Sample name:
data_313723_24_Cy5/data_313723_24_Cy3:BLOCK1
Background strain details: MEFs for our study were established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

growth_protocol: Cultured in DMEM supplemented with 10% FBS

value: Wild type #2

source_name: Dbp 4C from WT2 MEFs at circadian time 22 post dexamethasone synchronization


title: cells 40 hours post dexamethasone shock, biological rep3

description:
Sample name: CT40_3
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

source_name: Wild type mouse embryonic fibroblasts 40 hours post dexamethasone shock

tag: genotype/variation

value: 40 hours post dexamethasone shock


title: Dbp 4C WT CT30

description:
Sample name:
data_418203_WT3_30h_Rep1_Red_Cy5/data_418203_WT3_30h_Rep1_green_Cy3:BLOCK1
Background strain details: MEFs for our study were established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

treatment_protocol: Dexamethasone for 2 hours. Wash. Harvest after 30 hours

source_name: Dbp 4C from WT MEFs at circadian time 30 post dexamethasone synchronization


title: Dbp 4C WT2 CT34

description:
Sample name:
data_313805_36_Cy5/data_313805_36_Cy3:BLOCK1
Background strain details: MEFs for our study were established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

source_name: Dbp 4C from WT2 MEFs at circadian time 34 post dexamethasone synchronization


title: 19-B APE-8

description: Tagman-based qRT PCR

tag: age


title: 20-B APE-9

description: Tagman-based qRT PCR


title: 21-B Healthy control-5

description: Tagman-based qRT PCR

value: female


title: cells 40 hours post dexamethasone shock, biological rep2

description:
Sample name: CT40_2
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html


title: genomic DNA from liver sample 81

description: control

source_name: liver tissue 81

value: NORMAL


title: genomic DNA from liver sample 80

description: Healthy Obese

source_name: liver tissue 80

value: Healthy Obese


title: cells 40 hours post dexamethasone shock, biological rep1

description:
Sample name: CT40_1
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html


title: Dbp 4C WT CT22

description:
Sample name:
data_418193_WT1_22h_Rep1_Cy5/data_418193_WT1_22h_Rep1_Cy3:BLOCK1
Background strain details: MEFs for our study were established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

source_name: Dbp 4C from WT MEFs at circadian time 22 post dexamethasone synchronization


title: genomic DNA from liver sample 83

description: unknown

source_name: liver tissue 83


title: genomic DNA from liver sample 85

description: unknown

source_name: liver tissue 85


title: Chironomus riparius_moderate conc_cadmium_replicate 3

description: Chironomus riparius moderate conc.cadmium treated sample replicate 3

source_name: moderate conc. cadmium


title: 18-B APE-7

description: Tagman-based qRT PCR

source_name: Plasma


title: cells 46 hours post dexamethasone shock, biological rep2

description:
Sample name: CT46_2
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

source_name: Wild type mouse embryonic fibroblasts 46 hours post dexamethasone shock


title: cells 46 hours post dexamethasone shock, biological rep1

description:
Sample name: CT46_1
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html


title: Chironomus riparius_moderate conc_cadmium_replicate 4

description: Chironomus riparius moderate conc.cadmium treated sample replicate 4


title: Chironomus riparius_moderate conc_cadmium_replicate 5

description: Chironomus riparius moderate conc.cadmium treated sample replicate 5


title: genomic DNA from liver sample 84

description: unknown

source_name: liver tissue 84


title: 16-B APE-6

description: Tagman-based qRT PCR


title: Chironomus riparius_moderate conc_cadmium_replicate 6

description: Chironomus riparius moderate conc.cadmium treated sample replicate 6


title: cells 34 hours post dexamethasone shock, biological rep3

description:
Sample name: CT34_3
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

source_name: Wild type mouse embryonic fibroblasts 34 hours post dexamethasone shock

value: 34 hours post dexamethasone shock


title: 14-B APE-4

description: Tagman-based qRT PCR


title: 13-B APE-3

description: Tagman-based qRT PCR

value: male


title: cells 34 hours post dexamethasone shock, biological rep2

description:
Sample name: CT34_2
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html


title: 15-B APE-5

description: Tagman-based qRT PCR


title: 12-B APE-2

description: Tagman-based qRT PCR


title: genomic DNA from liver sample 76

description: NAFLD

source_name: liver tissue 76

value: NAFLD


title: cells 34 hours post dexamethasone shock, biological rep1

description:
Sample name: CT34_1
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

value: wild type


title: Chironomus riparius_low conc_cadmium_replicate 8

description: Chironomus riparius low  conc. cadmium treated sample replicate 8

source_name: low conc. cadmium

value: larvae


title: cells 30 hours post dexamethasone shock, biological rep2

description:
Sample name: CT30_2
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

source_name: Wild type mouse embryonic fibroblasts 30 hours post dexamethasone shock

value: 30 hours post dexamethasone shock

value: embryonic fibroblast


title: Chironomus riparius_moderate conc_cadmium_replicate 2

description: Chironomus riparius moderate conc.cadmium treated sample replicate 2


title: Chironomus riparius_moderate conc_cadmium_replicate 1

description: Chironomus riparius moderate conc. cadmium treated sample replicate 1


title: Chironomus riparius_low conc_cadmium_replicate 10

description: Chironomus riparius low  conc. cadmium treated sample replicate 10


title: cells 30 hours post dexamethasone shock, biological rep1

description:
Sample name: CT30_1
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html


title: Chironomus riparius_low conc_cadmium_replicate 7

description: Chironomus riparius low  conc. cadmium treated sample replicate 7


title: 10-B Healthy control-4

description: Tagman-based qRT PCR


title: 11-B APE-1

description: Tagman-based qRT PCR


title: cells 26 hours post dexamethasone shock, biological rep3

description:
Sample name: CT26_3
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

source_name: Wild type mouse embryonic fibroblasts 26 hours post dexamethasone shock

value: 26 hours post dexamethasone shock


title: cells 30 hours post dexamethasone shock, biological rep3

description:
Sample name: CT30_3
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html


title: Chironomus riparius_low conc_cadmium_replicate 9

description: Chironomus riparius low  conc. cadmium treated sample replicate 9


title: 9-B Healthy control-3

description: Tagman-based qRT PCR


title: genomic DNA from liver sample 79

description: NAFLD

source_name: liver tissue 79


title: 8-B Healthy control-2

description: Tagman-based qRT PCR


title: 7-B Healthy control-1

description: Tagman-based qRT PCR


title: cells 26 hours post dexamethasone shock, biological rep1

description:
Sample name: CT26_1
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html


title: cells 22 hours post dexamethasone shock, biological rep3

description:
Sample name: CT22_3
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html

source_name: Wild type mouse embryonic fibroblasts 22 hours post dexamethasone shock

value: 22 hours post dexamethasone shock


title: genomic DNA from liver sample 78

description: NASH

source_name: liver tissue 78

value: NASH


title: genomic DNA from liver sample 75

description: NASH

source_name: liver tissue 75


title: cells 22 hours post dexamethasone shock, biological rep1

description:
Sample name: CT22_1
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html


title: Chironomus riparius_low conc_cadmium_replicate 6

description: Chironomus riparius low  conc. cadmium treated sample replicate 6


title: cells 22 hours post dexamethasone shock, biological rep2

description:
Sample name: CT22_2
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html


title: genomic DNA from liver sample 74

description: Healthy Obese

source_name: liver tissue 74


title: cells 26 hours post dexamethasone shock, biological rep2

description:
Sample name: CT26_2
Background strain details: MEFs for our study established from two different C57BL/6 mice, as described previously in our lab. Briefly, mouse embryo fibroblast cultures were established by harvesting embryos at embryonic day 13. Head and liver removed, the remaining embryonic tissue was passed five times through an 18-gauge needle. The disrupted tissue was plated in DMEM + adequate supplements, (GibcoBRL) and cultured at 37°C in 5% CO2. For the WT and c/c MEFs, the media was supplemented with 10% FBS plus P/S. For the Bmal1 WT (used in the Affymetrix and in the Nimblegen microarrays) and KO MEFs (Used for two of the 4C Nimblegen microarrays), the media was supplemented with heat-inactivated 10% FBS plus aminoacids and P/S. The WT MEFs and the Bmal1-/- MEFs (those used in the text) where obtained from siblings coming from a mating system of mice described in http://jaxmice.jax.org/strain/009100.html .
The WT MEFs#2 used for two of the 4C Nimblegen arrays come from a mating of heterozygous mice described in http://jaxmice.jax.org/strain/002923.html


title: Chironomus riparius_low conc_cadmium_replicate 3

description: Chironomus riparius low  conc. cadmium treated sample replicate 3


title: Chironomus riparius_low conc_cadmium_replicate 4

description: Chironomus riparius low  conc. cadmium treated sample replicate 4


title: genomic DNA from liver sample 70

description: unknown

source_name: liver tissue 70

value: unknown


title: Chironomus riparius_low conc_cadmium_replicate 5

description: Chironomus riparius low  conc. cadmium treated sample replicate 5


title: genomic DNA from liver sample 72

description: Healthy Obese

source_name: liver tissue 72

value: liver


title: liver, H, A1649-14

city: Regensburg

first: Timo

last: Itzel

address: Franz-Josef-Strauß-Allee 11

institute: Universitätsklinikum Regensburg

hyb_protocol: according to the manufacturers protocols

data_processing: RMA normalization with Bioconductor package oligo

source_name: Healthy obese, after surgery

growth_protocol: liver biopsy

extract_protocol: For homogenisation of five to ten milligram frozen tissue and subsequent nucleic acid isolation, tubes with 1,4 mm ceramic beads (Precellys, Villeurbanne, France) and the AllPrep DNA/RNA Mini Kit (QIAGEN, Hilden, Germany) were used.

tag: tissue type

value: liver biopsy

value: Healthy obese

tag: fat

tag: inflammation

tag: bariatric surgery

value: after surgery

tag: Sex

tag: nas

tag: fibrosis

tag: lar

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin

tag: delta adipo


title: genomic DNA from liver sample 73

description: unknown

source_name: liver tissue 73

tag: group

tag: sex (1 - male, 2 - female)

tag: bariatric surgery (1 - before surgery, 2 - after)

tag: bmi

tag: tissue


title: liver, H, A1649-13

scan_protocol: according to the manufacturers protocols

tag: tissue type

tag: fat

tag: age


title: genomic DNA from liver sample 77

description: NASH

source_name: liver tissue 77


title: genomic DNA from liver sample 69

description: unknown

source_name: liver tissue 69


title: genomic DNA from liver sample 71

description: NAFLD

source_name: liver tissue 71


title: liver, N, A1649-11

source_name: Nash, after surgery

label_protocol: according to the manufacturers protocols

value: Nash

tag: inflammation

tag: bariatric surgery

tag: Sex

value: female


title: Chironomus riparius_low conc_cadmium_replicate 2

description: Chironomus riparius low  conc. cadmium treated sample replicate 2


title: bone macrophages, PAO-stimulated rep3

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: Quantile normalized the data using custom code originally provided by Kerby Shedden at the University of Michigan. The actual code used (in C++) is provided as a Series supplementary file [normalize2.Cpp.txt]. Please note that 'ProbeID' column in raw data files contains 'Array_Address_Id' identifiers.

label_protocol: According to Illumina protocol

growth_protocol: C57BL/6 mice were purchased from Jackson Laboratory (Bar Harbor, MA).  All mice were bred and maintained in a specific pathogen free environment in Baylor College of Medicine. C57BL/6 bone marrow derived macrophages were generated as previously described (PMID: 19016445). Briefly, marrow from femurs and tibias of 6-8 week old female mice were flushed and cultured at 37 deg in Dulbecco modified Eagle's minimal essential medium (DMEM) supplemented with 20% fetal calf serum (Invitrogen) and L929 fibroblast cell line secreting macrophage colony stimulating factor. After 5 days in culture, mature macrophages were harvested for further study.

extract_protocol: According to Illumina protocol. Total RNA was extracted with combination of RNA TRIzol reagent (Invitrogen) and the RNeasy Mini kit (QIAGEN).

treatment_protocol: Bone marrow derived macrophages from three animals were harvested and treated. C57BL/6 macrophages were stimulated at 37 deg for 24 hours with recombinant mouse/human IFN (20ng/mL; Applied Biosystems, Carlsbad,CA), lipopolysaccharide (LPS; 10ug/mL; SIGMA), PAO (10ug/mL) in CDMEM (DMEM, 10% FCS, 1% penicillin/streptomycin), or serum deficient media prior to phenotypic and functional characterization.  Murine experiments each involved three mice to generate biological replicates.

tag: strain

tag: genotype/variation

value: 6-8 week old

tag: gender

value: marrow from femurs and tibias

tag: cell type

value: bone marrow-derived macrophages (BMDMs)

tag: activated by

value: PAO (10ug/mL)


title: Chironomus riparius_solvent control_replicate 10

description: Chironomus riparius solvent control treated sample replicate 10

source_name: solvent control

value: larvae


title: bone macrophages, PAO-stimulated rep1

value: wild type


title: liver, H, A1359-64

source_name: Healthy obese

tag: nas

tag: fibrosis

tag: lar

tag: delta lar

tag: delta leptin

tag: leptin

tag: adiponectin

tag: delta adipo


title: bone macrophages, LPS-stimulated rep3

tag: age

tag: tissue

value: lipopolysaccharide (LPS; 10ug/mL)


title: bone macrophages, PAO-stimulated rep2