title: CDM-WT-30-B1b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 30 minutes after AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: Bulge basal cells, rep1

status: Public on Oct 19 2012

type: RNA

city: Brussels

first: KHALIL

last: KASS YOUSSEF

address: 808, Route de Lennick

country: Belgium

institute: ULB-IRIBHM

description: total RNA

hyb_protocol: 10  g labeled cRNA was hybridized for 16 hr at 45 C to mouse genome array MOE430a (Affymetrix).

scan_protocol: Processed chips were then read by an argon-ion laser confocal scanner (Genomics Core Facility, MSKCC). The entire procedure was repeated in duplicate for each sample to produce two independent datasets per mRNA sample.

data_processing: Raw microarray images were quantified using Gene Chip Operating Software (GCOS, Affymetrix). Analysis was performed with the R statistical environment (version 2.15.1) and the Bioconductor Affy package (version 1.36) (Irizarry et al, 2004). Normalization was run using affy package standard parameters (quantile normalization and RMA background correction).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: FACS sorted living GFP α6high CD34high expressing cells from postnatal d49 K14-GFP-actin mice.

label_protocol: mRNA were assessed by RNA 6000 Pico Assay (Agilent) and quantified spectrophotometrically. Primer olig0-dT-T7 (Genset) was used to reverse transcribe (SuperScript cDNA Synthesis Kit, Invitrogen) and then amplify (MessageAmp aRNA Kit, Ambion) 200 ng of RNA. Random  priming and biotinylated nucleotides were used to obtain cRNA for microarray.

extract_protocol: Absolutely RNA Kit (Stratagene)

tag: genotype/variation

value: K14-GFP-actin expressing

tag: tissue type

value: back skin

tag: cell type

value: basal bulge stem cells

tag: cell population

value: GFP α6high CD34high expressing


title: Total epidermis cells, rep2

description: total RNA

source_name: FACS sorted living total GFP expressing cells from postnatal d49 K14-GFP-actin mice.

value: total GFP expressing


title: genomic DNA from whole blood 37

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

description: normal whole blood sample

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 BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2. The raw data (non-normalized Unmethylated and Methylated signal intensities) are not available.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: whole blood 37

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from fresh frozen tissue using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

tag: sample type

value: whole blood

tag: plate

value: PLATE A

tag: sentrix barcode

tag: sentrix position

tag: well id

tag: age

tag: diseasestatus (1=control, 2=scz patient)

value: yes


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_28

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes. After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430.

data_processing: Data processing was done using open source statistical tool lumi package from Bioconductor. Data extraction was done for all beads individually, and outliers are removed when > 2.5 MAD (median absolute deviation). All remaining data points are used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated. Finally data was transformed using quantile normalization.

label_protocol: Total RNA was prepared for hybridization on Illumina Human Sentrix-12 BeadChip arrays (Illumina) according to manufacturer’s recommendations. In brief, 250 ng total RNA was used for cDNA synthesis, followed by the generation of biotin-labeled cRNA according to the MessageAmp II aRNA Amplification kit (Ambion).

growth_protocol: Frozen (n=98) prostate tumor and benign tissue samples were obtained from previously untreated patients, who had undergone radical prostatectomy after tumor diagnosis in a PSA based screening program performed in Tyrol by the Department of Urology, Medical University of Innsbruck (15). The study was approved by the ethics committee at the Medical University of Innsbruck. Immediately after surgery, the prostate specimens were rapidly processed for histopathological analysis and stored as either snap-frozen or fixed, paraffin-embedded tissue. Tissue samples were isolated from a cohort with Gleason scores (GS) between 6 and 10. Two subgroups were defined as low- (GS ≤ 3+4) and high-risk (GS ≥ 4+3). Apart from tumor foci, the corresponding benign tissue was collected from a subset of the same specimens. All tumor and benign areas were assigned by an experienced uropathologist, and tissue samples were isolated by macrodissection from 10µm cryo- or FFPE sections.

extract_protocol: Total RNA from frozen prostate tissues was isolated using EZ1 RNA Mini Kit (Qiagen) according to the manufacturer's instructions, quality checked by the Agilent 2100 Bioanalyzer (Agilent Technologies) and quantified.

tag: tissue

value: prostate

tag: disease stage

value: Cancer

tag: gleason pattern group

value: high


title: genomic DNA from whole blood 36

description: normal whole blood sample

source_name: whole blood 36

value: Male


title: genomic DNA from whole blood 38

description: normal whole blood sample

source_name: whole blood 38


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_25

value: low


title: CDM-KO-30-B1a

city: Philadelphia

first: Benjamin

last: Janto

state: PA

department: Microbiology & Immunology

institute: Drexel University College of Medicine

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled 30 minutes after AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

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

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

data_processing: Raw data (.pair file) was edited to remove subclusters (genes) that are not present in Haemophilus influenzae CZ4126/02 by merging it with a list of subclusters known to be present in CZ4126/02. The CZ4126/02-relevant data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Haemophilus influenzae

source_name: H. influenzae CZ4126/02 ΔLsr::Cmr, CDM, 30min after ODA600 0.75

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

growth_protocol: Haemophilus influenzae CZ4126/02 and Haemophilus influenzae CZ4126/02ΔLsr::Cmr were grown in either BHI or CDM (Coleman et al. J Clin Microbiol. 41 (9), 4408-10) to various culture densities using an inoculum from an overnight culture grown in BHI. 40 mL cultures were incubated at 37°C with shaking at 200 rpm.

extract_protocol: RNA was extracted using a Qiagen RNeasy Mini Plus kit with the standard protocol with gDNA eliminator columns. Eluted RNA (~85 µL) was DNased by adding 10 µL 10X TurboDNase buffer and 5 µL TurboDNase (2 units/µL) (Ambion) and incubating at 37 °C for 1.5 hours. 2 µL more TurboDNase was added and incubation was continued for an additional 1.5 hours. DNased RNA samples were cleaned by passing the samples through the RNeasy protocol a second time (with gDNA eliminator steps). Samples were eluted in nuclease-free (n.f.) water, quantitated on a NanoDrop 1000 spectrophotometer and stored at -80 °C. First- and second-strand cDNA synthesis was performed using a SuperScript® One-Cycle cDNA Kit (Invitrogen) as outlined in the NimbleGen Microarray Experienced User's Guide including RNase A and cDNA precipitation steps.

treatment_protocol: 2 mL of culture was diluted in 4 mL RNAProtect (Qiagen) and stored at RT for 10 minutes, then 4 °C overnight. Samples were pelleted, the supernatant removed and the cell pellets resuspended in 100 µL of 1X Tris-EDTA (TE) + 1 mg/mL lysozyme (Worthington Biochemical) and 1 mg/mL proteinase K (Qiagen).

tag: strain/background

tag: genotype

tag: growth medium

value: chemically-defined media (CDM)

tag: sampling time

value: 30 minutes after ODA600 0.75

tag: biological replicate

tag: technical replicate

tag: probe set


title: Total epidermis cells, rep1

description: total RNA

tag: genotype/variation

tag: tissue type

tag: cell type

tag: cell population


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_27

value: Benign


title: Bulge basal cells, rep2

description: total RNA

value: K14-GFP-actin expressing


title: genomic DNA from whole blood 39

description: normal whole blood sample

source_name: whole blood 39

tag: gender

tag: sample type

tag: plate

tag: sentrix barcode

tag: sentrix position

tag: well id


title: CDM-WT-30-A2b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 30 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

source_name: H. influenzae CZ4126/02 wild-type, CDM, 30min after ODA600 0.75

tag: strain/background

value: wild-type


title: CDM-WT-30-A2a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 30 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: genotype


title: genomic DNA from whole blood 34

description: normal whole blood sample

source_name: whole blood 34

tag: age

tag: diseasestatus (1=control, 2=scz patient)


title: genomic DNA from whole blood 35

description: normal whole blood sample

source_name: whole blood 35


title: CDM-WT-30-A1b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 30 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.

tag: growth medium

tag: sampling time

tag: biological replicate


title: CDM-WT-30-A1a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled 30 minutes after AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

tag: technical replicate

tag: probe set


title: genomic DNA from whole blood 32

description: normal whole blood sample

source_name: whole blood 32


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_19

tag: tissue

tag: disease stage

tag: gleason pattern group


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_18


title: genomic DNA from whole blood 33

description: normal whole blood sample

source_name: whole blood 33

tag: gender

tag: sample type


title: genomic DNA from whole blood 31

description: normal whole blood sample

source_name: whole blood 31

tag: plate

tag: sentrix barcode


title: CDM-KO-B2b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled before AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

source_name: H. influenzae CZ4126/02 ΔLsr::Cmr, CDM, ODA600 0.35


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_17


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_16


title: CDM-KO-B1b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled before AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: CDM-KO-B2a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled before AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: genomic DNA from whole blood 30

description: normal whole blood sample

source_name: whole blood 30

tag: sentrix position

tag: well id


title: genomic DNA from whole blood 28

description: normal whole blood sample

source_name: whole blood 28


title: genomic DNA from whole blood 27

description: normal whole blood sample

source_name: whole blood 27


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_14


title: genomic DNA from whole blood 29

description: normal whole blood sample

source_name: whole blood 29


title: CDM-KO-A2a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled before AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: strain/background

tag: genotype


title: CDM-KO-B1a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled before AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the second of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: CDM-KO-A2b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled before AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_15


title: CDM-KO-A1b

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled before AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: CDM-KO-A1a

description: This sample is of Haemophilus influenzae CZ4126/02ΔLsr::Cmr grown in chemically defined media and sampled before AI-2 uptake. This strain is a full locus deletion mutant in which the 9 genes of the Lsr locus (LsrKRACDBFGE) are deleted entirely. It is the first of two mutant strain biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_12


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_13


title: genomic DNA from whole blood 23

description: normal whole blood sample

source_name: whole blood 23

tag: age

tag: diseasestatus (1=control, 2=scz patient)


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_11


title: CDM-WT-B2b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled before AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.

source_name: H. influenzae CZ4126/02 wild-type, CDM, ODA600 0.35

tag: growth medium

tag: sampling time


title: CDM-WT-B2a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled before AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.

tag: biological replicate

tag: technical replicate


title: CDM-WT-B1b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled before AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.

tag: probe set


title: genomic DNA from whole blood 21

description: normal whole blood sample

source_name: whole blood 21


title: genomic DNA from whole blood 26

description: normal whole blood sample

source_name: whole blood 26

value: no


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_10

tag: tissue

tag: disease stage


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_09

tag: gleason pattern group


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_08


title: genomic DNA from whole blood 25

description: normal whole blood sample

source_name: whole blood 25

tag: gender

tag: sample type


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_24


title: CDM-WT-A2b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled before AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the second of two separate microarray chips.


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_07


title: CDM-WT-A2a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled before AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the second of two separate microarray chips.


title: CDM-WT-A1b

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled before AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the second of two identical probe sets represented on the first of two separate microarray chips.


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_05


title: genomic DNA from whole blood 20

description: normal whole blood sample

source_name: whole blood 20

tag: plate

tag: sentrix barcode


title: genomic DNA from whole blood 19

description: normal whole blood sample

source_name: whole blood 19

tag: sentrix position

tag: well id


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_06


title: CDM-WT-A1a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled before AI-2 uptake. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

tag: strain/background

tag: genotype


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_03


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_04


title: genomic DNA from whole blood 18

description: normal whole blood sample

source_name: whole blood 18

tag: age

tag: diseasestatus (1=control, 2=scz patient)


title: Human_Prostate_Tissue_Benign_IMGUS_DKFZ_01


title: Human_Prostate_Tissue_Tumor_IMGUS_DKFZ_02


title: Rat liver LE 100 TCDD 240 hours rep 1

status: Public on Oct 18 2012

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

description: Treated

data_processing: Raw OpenArray PCR data (Ct values) were loaded into the R statistical environment (v2.12.2). Data was normalized using reference genes Eef1a1, Gapdh, Hprt1, Pgk1, Ppia and Sdha and fold-changes calculated using the mean of the biological replicates (Treated - Control, in log2 space). Matrix non-normalized contains the mean of the raw Ct values. Matrix normalized contains values normalized to the  housekeeping genes (delta Ct). Fold Change contains values of treated animals compared to untreated animals (Ct[treated] - Ct[untreated]).

label: FAM

organism: Rattus norvegicus

source_name: liver, Long-Evans, 100 TCDD, 240 hour exposure

label_protocol: RNA was reverse-transcribed using High Capacity cDNA Reverse Transcription Kits (Applied Biosystems, Carlsbad, CA) following the manufacturer’s instructions, with the thermal cycler set to run at 25°C for 10 minutes, 37°C for 2 hours, 85°C for 5 minutes followed by a rapid cooling to 4°C. cDNA was sent to Life Technologies (Applied Biosystems, Carlsbad, CA) for PCR on the OpenArray system.

growth_protocol: Animals were housed in suspended, stainless-steel wire-mesh cages in groups of 4 rats with a 12h/12h light/dark cycle and with pelleted R36 feed and tap water. The temperature was maintained at  21 +/- 1 degree Celcius with relative humidity 50% +/- 10%.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini kits according to the manufacturer’s instructions (Qiagen, Mississauga, Canada). RNA was quantified using a NanoDrop UV spectrophotometer (Thermo Scientific, Mississauga, ON) and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Animals were treated with either TCDD or corn oil vehicle alone by oral gavage.

value: Liver

tag: strain

value: Long-Evans

value: 10-12 weeks

tag: treatment

value: 100 ug/kg TCDD

tag: exposure

value: 240 hours


title: genomic DNA from whole blood 22

description: normal whole blood sample

source_name: whole blood 22

value: Female

value: whole blood

value: PLATE A

value: yes


title: Rat liver LE 100 TCDD 240 hours rep 2

description: Treated

value: Male


title: Rat liver LE 100 TCDD 240 hours rep 4

description: Treated


title: Rat liver LE 100 TCDD 240 hours rep 3

description: Treated


title: genomic DNA from whole blood 17

description: normal whole blood sample

source_name: whole blood 17


title: genomic DNA from whole blood 11

description: normal whole blood sample

source_name: whole blood 11


title: Rat liver LE Corn oil 240 hours rep 10

description: Control

source_name: liver, Long-Evans, Corn oil treated, 240 hour exposure

value: Corn Oil vehicle


title: Rat liver LE Corn oil 240 hours rep 9

description: Control


title: Rat liver LE 100 TCDD 240 hours rep 5

description: Treated


title: genomic DNA from whole blood 24

description: normal whole blood sample

source_name: whole blood 24


title: CDM-WT-B1a

description: This sample is of wild-type Haemophilus influenzae CZ4126/02 grown in chemically defined media and sampled before AI-2 uptake. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures. This sample represents hybridization data from the first of two identical probe sets represented on the first of two separate microarray chips.

tag: growth medium

value: chemically-defined media (CDM)

tag: sampling time

tag: biological replicate

tag: technical replicate

tag: probe set


title: genomic DNA from whole blood 13

description: normal whole blood sample

source_name: whole blood 13

tag: gender

tag: sample type


title: P1 mouse eyeball extracted total RNA_Brg1_cKO3_GSM618320

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

hyb_protocol: 2.2 micrograms of cDNA was hybridized for 17 hr to the Affymetrix array as described in the Ovationâ¢ Biotin RNA Amplification and Labeling System manual. GenechipsÂ® were processed using protocol EukGE_WS2v4 450 for GenechipÂ® fluidics station 450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done across this data set togeteher with all .CEL files from the GSE25168 series by the RMA algorithm using GeneSpring GX11 program. No further adjustments were made to the data in the table.

source_name: P1 eyeball

label_protocol: 50 ng total RNA was amplified using the NUGEN Ovationâ¢ Biotin RNA Amplification and Labeling System. Amplified cDNA was fragmented and biotin labeled according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using RNeasy micro-elute columns (QIAGEN), according to manufacturer's instructions.

tag: genotype/variation

value: mixed background (Gebuhr TC, Kovalev GI, Bultman S, Godfrey V, Su L, Magnuson T. The role of Brg1, a catalytic subunit of mammalian chromatin-remodeling complexes, in T cell development. J Exp Med. 2003 Dec 15;198(12):1937-49.)


title: Rat liver LE Corn oil 240 hours rep 8

description: Control

tag: tissue


title: genomic DNA from whole blood 14

description: normal whole blood sample

source_name: whole blood 14

tag: plate

tag: sentrix barcode

tag: sentrix position

tag: well id


title: P1 mouse eyeball extracted total RNA_wt3_GSM618317

value: wildtype

tag: age


title: genomic DNA from whole blood 12

description: normal whole blood sample

source_name: whole blood 12

tag: diseasestatus (1=control, 2=scz patient)


title: genomic DNA from whole blood 15

description: normal whole blood sample

source_name: whole blood 15


title: Rat liver LE 100 TCDD 96 hours rep 4

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 96 hour exposure

tag: strain

tag: treatment

value: 96 hours


title: P1 mouse eyeball extracted total RNA_Brg1_cKO1_GSM618318


title: Rat liver LE Corn oil 240 hours rep 7

description: Control

tag: exposure


title: Rat liver LE 100 TCDD 96 hours rep 2

description: Treated


title: P1 mouse eyeball extracted total RNA_Brg1_cKO2_GSM618319


title: genomic DNA from whole blood 16

description: normal whole blood sample

source_name: whole blood 16


title: P1 mouse eyeball extracted total RNA_wt2_GSM618316


title: P1 mouse eyeball extracted total RNA_wt1_GSM618315


title: genomic DNA from whole blood 10

description: normal whole blood sample

source_name: whole blood 10


title: Rat liver LE Corn oil 96 hours rep 8

description: Control

source_name: liver, Long-Evans, Corn oil treated, 96 hour exposure


title: Rat liver LE Corn oil 96 hours rep 9

description: Control


title: Rat liver LE 100 TCDD 96 hours rep 1

description: Treated


title: genomic DNA from whole blood 7

description: normal whole blood sample

source_name: whole blood 7


title: Rat liver LE 100 TCDD 96 hours rep 3

description: Treated


title: Rat liver LE 1000 TCDD 19 hours rep 4

description: Treated

source_name: liver, Long-Evans, 1000 TCDD, 19 hour exposure

value: 1000 ug/kg TCDD

value: 19 hours


title: Rat liver LE Corn oil 96 hours rep 5

description: Control

value: Liver


title: Rat liver LE 1000 TCDD 19 hours rep 3

description: Treated

value: Long-Evans


title: Rat liver LE 1000 TCDD 19 hours rep 2

description: Treated

value: 10-12 weeks


title: P1 mouse eyeball extracted total RNA_wildtype4

hyb_protocol: 2.2 micrograms  of cDNA was hybridized for 17 hr to the Affymetrix MG_430A_2.0 array as described in the Ovation™ Biotin RNA Amplification and Labeling System manual.   Genechips® were processed using protocol EukGE_WS2v4 450 for Genechip® fluidics station 450.

label_protocol: 50 ng total RNA was amplified using the NUGEN Ovation™ Biotin RNA Amplification and Labeling System. Amplified cDNA was fragmented and biotin labeled according to manufacturer's instructions.

growth_protocol: Newborn Snf2h lens-conditional knockout and wildtype mouse pups were used.

extract_protocol: Total RNA was extracted  using RNeasy micro-elute columns (QIAGEN), according to manufacturer's instructions.

treatment_protocol: Newborn Snf2h lens-conditional knockout and wildtype mouse whole eyes were enucleated.

value: newborn


title: P1 mouse eyeball extracted total RNA_Snf2h_cKO4

value: Snf2h lens-conditional knockout


title: Rat liver LE 100 TCDD 19 hours rep 4

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 19 hour exposure

value: 100 ug/kg TCDD


title: Rat liver LE 1000 TCDD 19 hours rep 1

description: Treated


title: Rat liver LE 50 TCDD 19 hours rep 4

description: Treated

source_name: liver, Long-Evans, 50 TCDD, 19 hour exposure

value: 50 ug/kg TCDD


title: P1 mouse eyeball extracted total RNA_wildtype3


title: Rat liver LE 100 TCDD 19 hours rep 1

description: Treated


title: Rat liver LE 100 TCDD 19 hours rep 3

description: Treated


title: Rat liver LE 100 TCDD 19 hours rep 2

description: Treated


title: Rat liver LE 50 TCDD 19 hours rep 2

description: Treated


title: P1 mouse eyeball extracted total RNA_Snf2h_cKO1


title: P1 mouse eyeball extracted total RNA_Snf2h_cKO2


title: Rat liver LE Corn oil 96 hours rep 6

description: Control


title: P1 mouse eyeball extracted total RNA_Snf2h_cKO3


title: genomic DNA from whole blood 9

description: normal whole blood sample

source_name: whole blood 9

value: whole blood

value: PLATE A


title: Rat liver LE 50 TCDD 19 hours rep 3

description: Treated

value: Male


title: P1 mouse eyeball extracted total RNA_wildtype2


title: P1 mouse eyeball extracted total RNA_wildtype1


title: genomic DNA from whole blood 8

description: normal whole blood sample

source_name: whole blood 8

value: yes


title: Rat liver LE 50 TCDD 19 hours rep 1

description: Treated


title: Rat liver LE 10 TCDD 19 hours rep 4

description: Treated

source_name: liver, Long-Evans, 10 TCDD, 19 hour exposure

value: 10 ug/kg TCDD


title: Rat liver LE 10 TCDD 19 hours rep 3

description: Treated


title: Rat liver LE 10 TCDD 19 hours rep 2

description: Treated


title: Rat liver LE 10 TCDD 19 hours rep 1

description: Treated


title: Liver KK F rep3

city: San Antonio

first: Magalie

middle: S

last: Leduc

state: TX

institute: Texas Biomedical Research Institute

hyb_protocol: Following fragmentation and labeling, ~25ng/µl (according to manual) cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. (GeneChip Whole Transcript (WT) Sense Target Labeling Assay, Affymetrix 2005-2009) & (GeneChip Expression Wash, Stain and Scan User Manual, Affymetrix  2008)

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

data_processing: Average signal intensities for each probe set within arrays were calculated by the rma function provided within the affy package for R using a custom (Entrez Gene v13) CDF file (available via http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp).  The RMA method incorporates convolution background correction, sketch-quantile normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm.  For this experiment, six pairwise comparisons were used to statistically resolve gene/probe set expression differences between strains and genders using the R/maanova analysis package.  Specifically, differentially expressed genes/probe sets were detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package.  Statistical significance levels of the pairwise comparisons were calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method.  Differentially expressed genes/probe sets were declared at an FDR q-value threshold of 0.05.

source_name: liver tissue, KK/J strain, female

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix protocol from 300ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay, Affymetrix 2005-2009) & (GeneChip WT Terminal Labeling and Hybridization User Manual  2009-2011)

growth_protocol: The mice were kept on a chow diet until 8 weeks of age. They were separated individually for 3 days and fasted for 4 hours prior to the tissue collection. After sacrifice by cervical dislocation, the mice were perfused with PBS and the large lobe of the liver was collected.

extract_protocol: Trizol extraction of total RNA was performed using Ambion's PureLink RNA Mini Kit according to the manufacturer's instructions.

treatment_protocol: The large lobe of the liver was collected and kept in RNA later at room temperature for 24 hours and then kept at -80deg until RNA extraction

value: KK/HIJ

value: Female

value: liver


title: Rat liver LE 1 TCDD 19 hours rep 4

description: Treated

source_name: liver, Long-Evans, 1 TCDD, 19 hour exposure

value: 1 ug/kg TCDD


title: Rat liver LE 1 TCDD 19 hours rep 2

description: Treated

value: 19 hours


title: Rat liver LE 1 TCDD 19 hours rep 3

description: Treated

value: Liver


title: Rat liver LE 1 TCDD 19 hours rep 1

description: Treated

value: Long-Evans


title: Rat liver LE 0.1 TCDD 19 hours rep 3

description: Treated

source_name: liver, Long-Evans, 0.1 TCDD, 19 hour exposure

value: 10-12 weeks

value: 0.1 ug/kg TCDD


title: Rat liver LE 0.01 TCDD 19 hours rep 4

description: Treated

source_name: liver, Long-Evans, 0.01 TCDD, 19 hour exposure

value: 0.01 ug/kg TCDD


title: Rat liver LE 0.1 TCDD 19 hours rep 4

description: Treated


title: Rat liver LE 0.01 TCDD 19 hours rep 3

description: Treated


title: Liver B6 M rep3

source_name: liver tissue, C57BL/6J strain, male


title: Liver KK M rep2

source_name: liver tissue, KK/J strain, male


title: Liver B6 M rep2


title: Rat liver LE 0.01 TCDD 19 hours rep 2

description: Treated


title: Rat liver LE 0.01 TCDD 19 hours rep 1

description: Treated


title: Rat liver LE 0.1 TCDD 19 hours rep 1

description: Treated


title: Rat liver LE 0.1 TCDD 19 hours rep 2

description: Treated


title: Liver B6 F rep3

source_name: liver tissue, C57BL/6J strain, female


title: Liver B6 M rep1


title: Liver B6 F rep2


title: Liver KK F rep2


title: Liver KK M rep1


title: Liver KK F rep1


title: Rat liver LE 0.001 TCDD 19 hours rep 4

description: Treated

source_name: liver, Long-Evans, 0.001 TCDD, 19 hour exposure

value: 0.001 ug/kg TCDD


title: Tg muscle biological replicate 3

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description:
biological replicate 3
7917911031_H

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Image data were converted into unnormalized Sample Probe Profiles using the Illumina BeadStudio software and processed using the Model-Based Background Correction method (Xie, Wang, & Story, 2009). All gene expression values were log2 transformed and quantile normalized. Significance Analysis of Microarrays (Tusher, Tibshirani, & Chu, 2001) was used to identify differentially expressed genes among different groups using a false discovery rate of less than 10% and fold fold-change >2 as criteria.

source_name: gastrocnemius muscle

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

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

tag: genotype

tag: genetic background

value: 3 months

value: fed ad libitum

value: gastrocnemius muscle


title: Mdr1a Green tea polyphenols Low Rep1

city: Palmerston North

first: Helge

last: Dzierzon

address: Bachelar Road

department: Bioinformatics

country: New Zealand

institute: Plant and Food Research Ltd.

hyb_protocol: Labeled cRNAs were hybridised using an In Situ Hybridization Plus Kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer’s protocols, using 750 ng of experimental and reference cRNA onto 44k mouse oligonucleotide arrays (Agilent Technologies, Santa Clara, CA, USA). After hybridisation, slides were washed in solutions I, II and III (Agilent Technologies, Santa Clara, CA, USA) and air-dried.

scan_protocol: Slides were scanned using a GenePix Professional 4200A scanner (Molecular Devices, Sunnyvale, CA, USA) with photomultiplier tube (PMT) voltage of 580 V.   Spot identification and quantification was performed using GenePix 6.0 software (Molecular Devices).  All slides were individually checked and manually flagged for abnormalities.

data_processing: Microarray data were analysed using the Limma package in Bioconductor. Image analyses of the extracted foreground and background fluorescence intensity measurements were evaluated to select the best background correction for the experiment, but no background correction was necessary due to homogeneous hybridisation. Data were normalised using a local linear regression analysis (LOESS). Data with bad flags (-50 = poor or irregular spots, automatically flagged by the GenePix 4200A scanner; and -100, flagged by hand after visual inspection of the images) were not included in the analysis. Control probes (eQC, Bright corners, E1A and Pro25G) were also removed before normalization. Boxplots, density plots and spatial images of the raw and normalized data were examined in order to check the quality of the microarray data, and that no unusual results for any slide were observed. Data were log transformed before analysis and the mean difference between treatments calculated on this scale, resulting in a log ratio for each probe. The normalized values in the database consist of these log ratios. MA plots of the microarray data were drawn in order to check that there was no dependence of the log ratio on the intensity for any slide. The significance of the log ratio for each probe was determined by calculating one modified t-statistic per probe using an empirical Bayes approach.   The probability values were then corrected for multiple testing using the Benjamini and Hochberg correction, and a false discovery rate (FDR) calculated. Probes that had an FDR of less than 5 % (q<0*05) were considered to be differentially expressed between the groups fed the diets.

source_name: Swiss Mouse fed Green Tea extract (GrTP) diet (Colon Tissue)

label_protocol: cDNA and cRNA were synthesised using the Low RNA Input Linear Amplification kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer’s instructions. Reverse transcription used 500 ng of total RNA and oligo-dT primers. cRNA was synthesised and labeled with either cyanine3 (samples) or cyanine5 (reference) dye (Perkin-Elmer/NEN Life Science, Boston, MA, USA) and the dye incorporation evaluated using a Nanodrop ND-1000 spectrophotometer. Samples ranged from 10 to 22 pmol of dye/µg of RNA.

growth_protocol: Mice were weighed three times a week throughout the experiment to determine body weight changes. Food intake was measured during two periods of four days at 15 and 18 weeks of age. Food intake was calculated from the amount of food offered during the four days minus the remaining and spilt food at the end of the period. To minimize the variation between the last food intake and sampling, mice were fasted overnight before the tissue sampling and food was returned for two hours before sampling in the morning in staggered groups of six mice. Six mice from each dietary group were euthanised via CO2 asphyxiation and cervical dislocation at 21 weeks of age (sample group 1) and the remaining animals at 24 weeks of age (sample group 2). These time points were selected based on previous results to verify possible time-dependent changes in the colonic inflammation patterns.

extract_protocol: Total RNA was extracted from the colon tissues using Trizol (Invitrogen, Carlsbad, CA, USA) as described by the manufacturer, with a subsequent purification step using RNeasy columns (Qiagen, San Diego, CA, USA). RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and RNA quality was examined using a RNA 6000 LabChip Kit and a 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Twenty four male mdr1a-/- mice, five to six weeks old, mean weight 23.8 g (SD 0.6 g), were housed individually in cages with pressed wood chips and a plastic tube for environmental enrichment. The room was climate controlled (22 to 24 ºC, at approximately 60 % humidity) with a 12-hour light:dark cycle. All mice were acclimatized for a week before the start of the experiment. Mice were randomly assigned to three treatment groups of 12 animals each. Each treatment group received one of the following diets:  Control (AIN-76A powdered diet) - Microarray Slides 251269421243,251269421255, 251269421259 & 251269421253 (4 mice with a high histology score were selected for microarray analysis)  Green Tea extract (AIN-76A + 0.6 %Green Tea extract containing 35% epigallocatechin gallate LKT laboratories (St Paul, MN, USA). Microarray slides: 251269421251, 251269421280, 251269421283 & 251269421360 (4 mice with a low histology score were selected for microarray analysis). Animals received food and water ad libitum.

value: Swiss mouse

value: wild type

value: male

value: 7 weeks

value: colon tissue

source_name: mdr1a-/- fed Green Tea extract (GrTP) diet (colon tissue)


title: Mdr1a Green tea polyphenols Low Rep3


title: Liver KK M rep3

value: KK/HIJ

value: Male

value: liver


title: Liver B6 F rep1

value: Female


title: Rat liver LE 0.001 TCDD 19 hours rep 2

description: Treated

value: Liver

value: Long-Evans

value: 19 hours


title: Mdr1a Green tea polyphenols Low Rep2


title: Mdr1a Green tea polyphenols Low Rep4


title: Rat liver LE 0.001 TCDD 19 hours rep 1

description: Treated

value: 10-12 weeks


title: Tg muscle biological replicate 2

description:
biological replicate 2
7917911031_G


title: Rat liver LE Corn oil 19 hours rep 7

description: Control

source_name: liver, Long-Evans, Corn oil treated, 19 hour exposure

value: Corn Oil vehicle


title: Rat liver LE 0.001 TCDD 19 hours rep 3

description: Treated

value: 0.001 ug/kg TCDD


title: Rat liver LE Corn oil 19 hours rep 5

description: Control


title: Rat liver LE Corn oil 19 hours rep 6

description: Control


title: Rat liver LE Corn oil 19 hours rep 4

description: Control


title: Rat liver LE Corn oil 19 hours rep 3

description: Control


title: WT control for Tg muscle biological replicate 2

description:
biological replicate 2
7917911031_D

value: Wild-type

value: 3 months

value: fed ad libitum


title: Tg muscle biological replicate 1

description:
biological replicate 1
7917911031_F

value: gastrocnemius muscle


title: WT control for Tg muscle biological replicate 3

description:
biological replicate 3
7917911031_E


title: WT control for Tg muscle biological replicate 1

description:
biological replicate 1
7917911031_C


title: Tg eWAT biological replicate 3

description:
biological replicate 3
7917911031_B

source_name: epididymal white adipose tissue

value: epididymal white adipose tissue


title: Rat liver LE Corn oil 19 hours rep 1

description: Control


title: Rat liver LE Corn oil 19 hours rep 2

description: Control


title: daf-9 mutant T2B

city: kunming

first: yi

middle: cheng

last: ma

state: Yunnan

address: No.2 North Cuihu Road

country: China

institute: Lab for Conservation and Utilization of Bio-Resources

description: This sample is of C.elegans  daf-9(e1406) loss of function mutant. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit.

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.

organism: Caenorhabditis elegans

source_name: C.elegans daf-9 mutant

label_protocol: NimbleGen One-Color DNA Labeling Kit was used for sample labeling.

growth_protocol: C.elegans wild-type ,daf-9(e1406)mutant and daf-12(rh411rh61) were grown to L4 at 20°C in NGM media .Then they infected 24 hours by P. aeruginosa respectively.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. About 5 μg total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit.

value: whole organism

tag: developmental stage

value: daf-9 mutant


title: daf-12 mutant T3C

description: This sample is of C.elegans daf-12(rh411rh61) loss of function mutant. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.

source_name: C.elegans daf-12 mutant

value: daf-12 mutant


title: daf-9 mutant T3B

description: This sample is of C.elegans  daf-9(e1406) loss of function mutant. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: daf-12 mutant T1C

description: This sample is of C.elegans daf-12(rh411rh61) loss of function mutant. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: LPS-stimulated tnc-/- BMDMs

city: London

first: Kim

middle: S.

last: Midwood

address: 65 Aspenlea Road

country: United Kingdom

institute: Kennedy Institute of Rheumatology

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using the SDS software (Applied Biosystems).
For the normalization it uses the housekeeping gene: MammU6.
Relative Quantification (RQ) using Comparative CT was used to determine the change in expression of a nucleic acid sequence (target) in a test sample relative to the same sequence in a calibrator sample. The calibrator sample was a non-stimulated control (i.e. non-stimulated tnc+/+ BMDMs and non-stimulated tnc-/- BMDMs).
The SDS software (Applied Biosystems) automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data. Fold Change worksheet reports test/control (i.e., LPS-stimulated tnc+/+/non-stimulated tnc+/+ and LPS-stimulated tnc-/-/non-stimulated tnc-/-) ratios.

source_name: LPS-stimulated tnc-/- BMDMs

label_protocol: miRNA profile was analysed using the TaqMan Low Density Arrays (Applied Biosystems) following the Manufacturer’s instructions. Reverse transcription was performed from 1000 ng total RNA using Megaplex RT Primers & TaqMan MicroRNA Reverse Transcription kit (Applied Biosystems). Quantitative real-time PCR was performed (Applied Biosystems 7900HT Fast Real-Time PCR System) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.

growth_protocol: BMDMs grown in culture in DMEM medium containing 10% FCS and 1% penicillin/streptomycin.

extract_protocol: Total RNA was extracted using the standard TRIZOL protocol.

treatment_protocol: 100ng/ml LPS for 8 hours.

tag: cell type

value: Bone marrow-derived macrophages

value: tnc-/-

tag: activation agent

value: LPS

tag: time

value: 8 hours


title: wild-type T1A

description: This sample is of  C.elegans wild-type  . It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: C.elegans wild-type

value: wild-type


title: Tg eWAT biological replicate 1

description:
biological replicate 1
7917911014_H


title: LPS-stimulated tnc+/+ BMDMs

description: Test

source_name: LPS-stimulated tnc+/+ BMDMs

tag: genotype/variation

value: tnc+/+


title: genomic DNA from whole blood 6

description: normal whole blood sample

source_name: whole blood 6

tag: gender

value: Male

tag: sample type

value: whole blood

value: PLATE A

value: yes


title: WT control for Tg eWAT biological replicate 2

description:
biological replicate 2
7917911014_F

value: Wild-type

value: 3 months

tag: tissue


title: daf-9 mutant T1B

description: This sample is of C.elegans daf-9(e1406) loss of function mutant. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: Rat liver LE 100 TCDD 10 hours rep 4

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 10 hour exposure

value: Liver

value: Long-Evans

value: 10-12 weeks

value: 100 ug/kg TCDD

value: 10 hours


title: daf-12 mutant T2C

description: This sample is of C.elegans daf-12(rh411rh61) loss of function mutant. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.

value: whole organism

value: daf-12 mutant


title: WT control for Tg eWAT biological replicate 3

description:
biological replicate 3
7917911014_G

value: fed ad libitum

value: epididymal white adipose tissue


title: wild-type T2A

description: This sample is of  C.elegans wild-type  . It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

value: wild-type


title: Rat liver LE 100 TCDD 10 hours rep 3

description: Treated


title: Tg eWAT biological replicate 2

description:
biological replicate 2
7917911031_A


title: non-stimulated tnc-/- BMDMs

description: Control

source_name: non-stimulated tnc-/- BMDMs

treatment_protocol: None.

value: Bone marrow-derived macrophages

value: tnc-/-

value: 8 hours


title: wild-type T3A

description: This sample is of  C.elegans wild-type  . It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: non-stimulated tnc+/+ BMDMs

description: Control

source_name: non-stimulated tnc+/+ BMDMs

value: tnc+/+


title: Rat liver LE 100 TCDD 10 hours rep 2

description: Treated

value: Male


title: Rat liver LE 100 TCDD 240 hours rep 4

description: Treated

data_processing: Raw qPCR data (Ct values) were loaded into the R statistical environment (v2.12.2). Wells flagged with Non-Amplified Well were removed prior to downstream analysis. Data was normalized using reference genes Gapdh and Pgk1 and fold-changes calculated using the mean of the biological replicates (Treated - Control, in log2 space). Matrix non-normalized contains the mean of the raw Ct values. Matrix normalized contains values normalized to the  housekeeping genes (delta Ct). Fold Change contains values of treated animals compared to untreated animals (Ct[treated] - Ct[untreated]).

source_name: liver, Long-Evans, 100 TCDD, 240 hour exposure

label_protocol: RNA was reverse-transcribed using High Capacity cDNA Reverse Transcription Kits (Applied Biosystems, Carlsbad, CA) following the manufacturer’s instructions, with the thermal cycler set to run at 25°C for 10 minutes, 37°C for 2 hours, 85°C for 5 minutes followed by a rapid cooling to 4°C. qPCR was performed using the 7900HT Fast Real-Time PCR System (Applied Biosystems, Carlsbad, CA) using the ΔΔCT standard 384-well PCR plate settings; an initial 2-minute hold at 50°C was performed to ensure that any UTP-containing contaminants from previous PCR reactions were fully digested by the AmpErase UNG nuclease. Polymerase was activated by a 10-minute hold at 95°C and reactions carried out by 40 cycles of 15 seconds at 95°C and 1 minute at 60°C

value: 240 hours


title: Rat liver LE 100 TCDD 10 hours rep 1

description: Treated


title: Rat liver LE 100 TCDD 240 hours rep 5

description: Treated


title: Rat liver LE 100 TCDD 240 hours rep 1

description: Treated


title: Rat liver LE 100 TCDD 240 hours rep 3

description: Treated


title: Rat liver LE 100 TCDD 240 hours rep 2

description: Treated


title: Tg Liver biological replicate 1

description:
biological replicate 1
7917911014_B

source_name: liver

value: 3 months

value: liver


title: WT control for Tg eWAT biological replicate 1

description:
biological replicate 1
7917911014_E

value: Wild-type


title: Tg Liver biological replicate 2

description:
biological replicate 2
7917911014_C


title: Rat liver LE 100 TCDD 6 hours rep 3

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 6 hour exposure

value: Liver

value: Long-Evans

value: 10-12 weeks

value: 6 hours


title: WT control for Tg Liver biological replicate 3

description:
biological replicate 3
7917911014_A


title: WT control for Tg Liver biological replicate 2

description:
biological replicate 2
7917911007_H


title: Rat liver LE 100 TCDD 96 hours rep 3

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 96 hour exposure

value: 100 ug/kg TCDD

value: 96 hours


title: Rat liver LE Corn oil 240 hours rep 7

description: Control

source_name: liver, Long-Evans, Corn oil treated, 240 hour exposure

value: Corn Oil vehicle


title: Rat liver LE 100 TCDD 96 hours rep 2

description: Treated


title: Rat liver LE 100 TCDD 6 hours rep 1

description: Treated


title: Rat liver LE 100 TCDD 6 hours rep 2

description: Treated


title: WT control for Tg Liver biological replicate 1

description:
biological replicate 1
7917911007_G

value: fed ad libitum


title: Rat liver LE 100 TCDD 96 hours rep 4

description: Treated


title: Rat liver LE Corn oil 240 hours rep 9

description: Control


title: Rat liver LE 100 TCDD 96 hours rep 1

description: Treated


title: Rat liver LE 100 TCDD 3 hours rep 4

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 3 hour exposure

value: 3 hours


title: WT CR muscle biological replicate 4

description:
biological replicate 4
7917911007_F

source_name: gastrocnemius muscle

value: 40% calorie restriction for 2 wks

value: gastrocnemius muscle


title: WT CR muscle biological replicate 3

description:
biological replicate 3
7917911007_E


title: Rat liver LE Corn oil 240 hours rep 11

description: Control


title: Rat liver LE 100 TCDD 6 hours rep 4

description: Treated


title: Rat liver LE 100 TCDD 3 hours rep 3

description: Treated


title: Rat liver LE Corn oil 240 hours rep 8

description: Control


title: Rat liver LE Corn oil 96 hours rep 6

description: Control

source_name: liver, Long-Evans, Corn oil treated, 96 hour exposure


title: Rat liver LE Corn oil 96 hours rep 8

description: Control


title: Rat liver LE Corn oil 96 hours rep 9

description: Control


title: WT CR muscle biological replicate 2

description:
biological replicate 2
7917911007_D


title: WT CR muscle biological replicate 1

description:
biological replicate 1
7917911007_C


title: Rat liver LE 100 TCDD 3 hours rep 2

description: Treated


title: WT Fast muscle biological replicate 3

description:
biological replicate 3
7917911007_B

value: fasted 24 hr


title: Rat liver LE Corn oil 96 hours rep 5

description: Control

value: Male


title: Rat liver LE 1000 TCDD 19 hours rep 4

description: Treated

source_name: liver, Long-Evans, 1000 TCDD, 19 hour exposure

value: 1000 ug/kg TCDD

value: 19 hours


title: Rat liver LE 100 TCDD 3 hours rep 1

description: Treated


title: Rat liver LE 1000 TCDD 19 hours rep 2

description: Treated


title: Rat liver LE 1000 TCDD 19 hours rep 3

description: Treated


title: Rat liver HW 100 TCDD 384 hours rep 4

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 384 hour exposure

value: Han/Wistar

value: 384 hours


title: Rat liver HW 100 TCDD 384 hours rep 3

description: Treated

value: Liver


title: WT Fast muscle biological replicate 2

description:
biological replicate 2
7917911007_A

value: Wild-type

value: 3 months


title: Rat liver LE 1000 TCDD 19 hours rep 1

description: Treated

value: Long-Evans

value: 10-12 weeks


title: Rat liver LE 100 TCDD 19 hours rep 3

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 19 hour exposure

value: 100 ug/kg TCDD


title: Rat liver LE 100 TCDD 19 hours rep 1

description: Treated


title: Rat liver LE 100 TCDD 19 hours rep 2

description: Treated


title: WT Fast muscle biological replicate 1

description:
biological replicate 1
7917911004_H


title: Rat liver LE 50 TCDD 19 hours rep 4

description: Treated

source_name: liver, Long-Evans, 50 TCDD, 19 hour exposure

value: 50 ug/kg TCDD


title: WT AL muscle biological replicate 3

description:
biological replicate 3
7917911004_G

value: fed ad libitum


title: Rat liver LE 50 TCDD 19 hours rep 3

description: Treated


title: Rat liver HW 100 TCDD 384 hours rep 2

description: Treated


title: WT AL muscle biological replicate 2

description:
biological replicate 2
7917911004_F


title: Rat liver HW 100 TCDD 384 hours rep 1

description: Treated


title: Rat liver LE 50 TCDD 19 hours rep 2

description: Treated


title: WT AL muscle biological replicate 1

description:
biological replicate 1
7917911004_E


title: Rat liver LE 50 TCDD 19 hours rep 1

description: Treated


title: Rat liver LE 100 TCDD 19 hours rep 4

description: Treated


title: Rat liver HW Corn oil 384 hours rep 4

description: Control

source_name: liver, Han/Wistar, Corn oil treated, 384hour exposure

value: Corn Oil vehicle


title: Rat liver HW Corn oil 384 hours rep 3

description: Control


title: Rat liver LE 10 TCDD 19 hours rep 2

description: Treated

source_name: liver, Long-Evans, 10 TCDD, 19 hour exposure

value: 10 ug/kg TCDD


title: Rat liver LE 10 TCDD 19 hours rep 3

description: Treated


title: Rat liver LE 10 TCDD 19 hours rep 4

description: Treated


title: WT CR eWAT biological replicate 3

description:
biological replicate 3
7917911004_C

source_name: epididymal white adipose tissue

value: 40% calorie restriction for 2 wks

value: epididymal white adipose tissue


title: Rat liver LE 10 TCDD 19 hours rep 1

description: Treated

value: Male


title: WT CR eWAT biological replicate 4

description:
biological replicate 4
7917911004_D


title: Rat liver HW Corn oil 384 hours rep 2

description: Control


title: Tg Liver biological replicate 3

description:
biological replicate 3
7917911014_D

value: liver


title: WT CR eWAT biological replicate 2

description:
biological replicate 2
7917911004_B


title: Rat liver LE 1 TCDD 19 hours rep 4

description: Treated

source_name: liver, Long-Evans, 1 TCDD, 19 hour exposure

value: 1 ug/kg TCDD

value: 19 hours


title: Rat liver LE 1 TCDD 19 hours rep 3

description: Treated


title: Rat liver LE 1 TCDD 19 hours rep 1

description: Treated


title: WT Fast eWAT biological replicate 3

description:
biological replicate 3
7539447027_H

value: fasted 24 hr


title: Rat liver LE 0.1 TCDD 19 hours rep 3

description: Treated

source_name: liver, Long-Evans, 0.1 TCDD, 19 hour exposure

value: Liver

value: 0.1 ug/kg TCDD


title: Rat liver LE 0.1 TCDD 19 hours rep 2

description: Treated


title: Rat liver LE 0.1 TCDD 19 hours rep 1

description: Treated


title: WT CR eWAT biological replicate 1

description:
biological replicate 1
7917911004_A

value: Wild-type

value: 3 months


title: WT Fast eWAT biological replicate 2

description:
biological replicate 2
7539447027_G


title: Rat liver LE 0.001 TCDD 19 hours rep 4

description: Treated

source_name: liver, Long-Evans, 0.001 TCDD, 19 hour exposure

value: Long-Evans

value: 10-12 weeks

value: 0.001 ug/kg TCDD


title: Rat liver LE 1 TCDD 19 hours rep 2

description: Treated


title: Rat liver LE 0.01 TCDD 19 hours rep 2

description: Treated

source_name: liver, Long-Evans, 0.01 TCDD, 19 hour exposure

value: 0.01 ug/kg TCDD


title: Rat liver LE 0.01 TCDD 19 hours rep 1

description: Treated


title: Rat liver LE 0.001 TCDD 19 hours rep 3

description: Treated


title: Rat liver LE Corn oil 19 hours rep 6

description: Control

source_name: liver, Long-Evans, Corn oil treated, 19 hour exposure

value: Corn Oil vehicle


title: WT AL eWAT biological replicate 2

description:
biological replicate 2
7539447027_D

value: fed ad libitum


title: Rat liver LE Corn oil 19 hours rep 7

description: Control


title: Rat liver LE 0.001 TCDD 19 hours rep 2

description: Treated


title: Rat liver LE 0.001 TCDD 19 hours rep 1

description: Treated


title: Rat liver LE Corn oil 240 hours rep 10

description: Control

value: 240 hours


title: Rat liver LE 0.1 TCDD 19 hours rep 4

description: Treated


title: Rat liver LE Corn oil 19 hours rep 5

description: Control


title: WT AL eWAT biological replicate 1

description:
biological replicate 1
7539447027_C

value: epididymal white adipose tissue


title: Rat liver LE 0.01 TCDD 19 hours rep 4

description: Treated

value: Male


title: WT AL eWAT biological replicate 3

description:
biological replicate 3
7539447027_E


title: Rat liver LE 0.01 TCDD 19 hours rep 3

description: Treated


title: Rat liver LE Corn oil 19 hours rep 4

description: Control


title: Rat liver LE Corn oil 19 hours rep 3

description: Control


title: WT CR Liver biological replicate 3

description:
biological replicate 3
7539447027_A

source_name: liver

value: 40% calorie restriction for 2 wks

value: liver


title: Rat liver LE Corn oil 19 hours rep 2

description: Control

value: 19 hours


title: Rat liver HW 100 TCDD 96 hours rep 5

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 96 hour exposure

value: Han/Wistar

value: 100 ug/kg TCDD

value: 96 hours


title: WT CR Liver biological replicate 4

description:
biological replicate 4
7539447027_B

value: Wild-type


title: Rat liver HW 100 TCDD 96 hours rep 4

description: Treated

value: Liver


title: Rat liver HW 100 TCDD 96 hours rep 3

description: Treated


title: WT Fast Liver biological replicate 3

description:
biological replicate 3
7539447003_F

value: 3 months

value: fasted 24 hr


title: Rat liver LE Corn oil 19 hours rep 1

description: Control

value: Long-Evans

value: 10-12 weeks


title: WT CR Liver biological replicate 1

description:
biological replicate 1
7539447003_G


title: WT Fast eWAT biological replicate 1

description:
biological replicate 1
7539447027_F


title: Rat liver LE 100 TCDD 6 hours rep 4

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 6 hour exposure

value: 6 hours


title: Rat liver LE 100 TCDD 6 hours rep 3

description: Treated


title: Rat liver LE 100 TCDD 6 hours rep 1

description: Treated


title: Rat liver LE 100 TCDD 10 hours rep 1

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 10 hour exposure

value: 10 hours


title: Rat liver HW 100 TCDD 96 hours rep 1

description: Treated


title: Rat liver HW 100 TCDD 96 hours rep 2

description: Treated


title: Rat liver LE 100 TCDD 10 hours rep 2

description: Treated


title: WT CR Liver biological replicate 2

description:
biological replicate 2
7539447003_H


title: Rat liver LE 100 TCDD 10 hours rep 3

description: Treated


title: Rat liver LE 100 TCDD 3 hours rep 3

description: Treated

source_name: liver, Long-Evans, 100 TCDD, 3 hour exposure

value: 3 hours


title: Rat liver LE 100 TCDD 10 hours rep 4

description: Treated


title: Rat liver LE 100 TCDD 6 hours rep 2

description: Treated


title: Rat liver LE 100 TCDD 3 hours rep 4

description: Treated


title: WT Fast Liver biological replicate 2

description:
biological replicate 2
7539447003_E


title: WT Fast Liver biological replicate 1

description:
biological replicate 1
7539447003_D


title: Rat liver LE 100 TCDD 3 hours rep 2

description: Treated


title: WT AL Liver biological replicate 2

description:
biological replicate 2
7539447003_B

value: fed ad libitum


title: WT AL Liver biological replicate 3

description:
biological replicate 3
7539447003_C


title: Rat liver LE 100 TCDD 3 hours rep 1

description: Treated

value: Male


title: Rat liver HW Corn oil 96 hours rep 4

description: Control

source_name: liver, Han/Wistar, Corn oil treated, 96 hour exposure

value: Corn Oil vehicle


title: Rat liver HW Corn oil 96 hours rep 5

description: Control


title: Rat liver HW Corn oil 96 hours rep 3

description: Control


title: Rat liver HW Corn oil 96 hours rep 2

description: Control


title: Rat liver HW 100 TCDD 384 hours rep 4

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 384 hour exposure

value: 384 hours


title: Rat liver HW 100 TCDD 384 hours rep 3

description: Treated


title: Rat liver HW 100 TCDD 384 hours rep 2

description: Treated


title: Rat liver HW 100 TCDD 384 hours rep 1

description: Treated


title: Rat liver HW 3000 TCDD 19 hours rep 3

description: Treated

source_name: liver, Han/Wistar, 3000 TCDD, 19 hour exposure

value: 3000 ug/kg TCDD

value: 19 hours


title: Rat liver HW 3000 TCDD 19 hours rep 4

description: Treated

value: Han/Wistar


title: Rat liver HW 3000 TCDD 19 hours rep 2

description: Treated


title: Rat liver HW Corn oil 384 hours rep 1

description: Control


title: Rat liver HW Corn oil 384 hours rep 3

description: Control


title: Rat liver HW Corn oil 384 hours rep 4

description: Control


title: WT AL Liver biological replicate 1

description:
biological replicate 1
7539447003_A

value: liver


title: TGFb1_LPS_IFNg_4

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: BeadStudio, quantile normalization

label: Biotin

source_name: Primary cortical astrocytes treated with TGF-b1 + LPS + IFNg

label_protocol: Illumina protocol

growth_protocol: Primary astrocyte cultures were prepared from cerebral cortices of postnatal (1-3 days) C57Bl/6 mice as previously described (Hamby et al., 2006a; Hamby et al., 2006b). In brief, plating media consisted of  L-glutamine-free DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS, Hyclone), 10% calf serum (CS, Hyclone), 2mM L-glutamine, 50 IU/ml penicillin, 50µg/ml streptomycin, and 10ng/ml epidermal growth factor (EGF). Upon confluence, astrocyte cultures were purified of microglia by treatment with 8µM cytosine β-D-arabinofuranoside (Ara-C; Sigma) for 5-6 days to substantially reduce microglia followed by treatment with 75mM L-leucine methyl ester (LME, Sigma; 60-90min) one day prior to experimentation to completely eradicate any residual microglia. Cells were maintained in medium consisting of L-glutamine-free DMEM, 10% CS, 2mM L-glutamine, 50 IU/ml penicillin and 50µg/ml streptomycin. All cultures were maintained at 37°C in a humidified atmosphere of 6% CO2 and used after 14-31 days in vitro.

extract_protocol: Total RNA was isolated from astrocytes using the Qiagen RNeasy Kit. RNA quantity and quality was assessed using a Nanodrop (Nanodrop Technologies) and the Agilent Bioanalyzer (Agilent Technologies), respectively. Total RNA (200ng) was amplified, biotinylated and hybridized on Illumina Mouseref-8 v2.0 BeadChip arrays. Slides were scanned using Illumina BeadStation and signal extracted using the Illumina BeadStudio software (Illumina, San Diego CA).

treatment_protocol: Purified astrocyte cultures were exposed to four different experimental stimulation conditions. (i) Basal; consisting of 32hr in stimulation medium (L-glutamine-free DMEM supplemented with 5% CS, 2mM L-glutamine, 50 IU/ml penicillin, and 50μg/ml streptomycin). (ii) TGF-β1; consisting of 32hr in stimulation medium with TGF-β1 (3ng/ml; human recombinant; R&D Systems) (iii) LPS+IFNγ; consisting of 24hr in stimulation medium prior to addition of 2µg/ml LPS (E.coli 0127:B8, Sigma) and 3ng/ml IFNγ (recombinant mouse, R&D Systems) for a further 8hr.  (iv) TGFβ+LPS+IFNγ; consisting of 24hr in stimulation medium with TGF-β1 prior to addition of LPS+IFNγ for a further 8hr. The 24hr duration of TGF-β1 treatment was chosen on the basis of previous experiments showing a maximal and stable effect of TGF-β on induction of iNOS and enhancement of nitric oxide production in purified astrocyte cultures over this time period (Hamby et al., 2006a).

tag: replicate

value: Primary cortical astrocytes

value: TGF-b1 + LPS + IFNg


title: Rat liver HW 1000 TCDD 19 hours rep 3

description: Treated

source_name: liver, Han/Wistar, 1000 TCDD, 19 hour exposure

value: Liver

value: 1000 ug/kg TCDD


title: Rat liver HW 1000 TCDD 19 hours rep 4

description: Treated


title: Rat liver HW 3000 TCDD 19 hours rep 1

description: Treated


title: Rat liver HW 1000 TCDD 19 hours rep 2

description: Treated


title: LPS_IFNg_4

source_name: Primary cortical astrocytes treated with LPS + IFNg

value: LPS + IFNg


title: TGFb1_4

source_name: Primary cortical astrocytes treated with TGF-b1


title: TGFb1_LPS_IFNg_3


title: LPS_IFNg_3


title: Rat liver HW 1000 TCDD 19 hours rep 1

description: Treated

value: 10-12 weeks


title: BASAL_4

source_name: Primary cortical astrocytes treated with BASAL

value: BASAL


title: Rat liver HW Corn oil 384 hours rep 2

description: Control

source_name: liver, Han/Wistar, Corn oil treated, 384hour exposure


title: Rat liver HW 100 TCDD 96 hours rep 5

description: Treated

value: 100 ug/kg TCDD

value: 96 hours


title: TGFb1_3


title: Rat liver HW 100 TCDD 19 hours rep 4

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 19 hour exposure


title: TGFb1_LPS_IFNg_2


title: Rat liver HW 100 TCDD 96 hours rep 3

description: Treated


title: BASAL_3


title: Rat liver HW 100 TCDD 19 hours rep 3

description: Treated


title: Rat liver HW 100 TCDD 96 hours rep 1

description: Treated


title: Rat liver HW Corn oil 96 hours rep 5

description: Control


title: Rat liver HW 100 TCDD 96 hours rep 2

description: Treated


title: Rat liver HW Corn oil 96 hours rep 4

description: Control


title: Rat liver HW Corn oil 96 hours rep 3

description: Control


title: Rat liver HW 100 TCDD 19 hours rep 1

description: Treated


title: Rat liver HW Corn oil 96 hours rep 2

description: Control


title: Rat liver HW Corn oil 96 hours rep 1

description: Control


title: Rat liver HW 10 TCDD 19 hours rep 4

description: Treated

source_name: liver, Han/Wistar, 10 TCDD, 19 hour exposure

value: 10 ug/kg TCDD


title: Rat liver HW 10 TCDD 19 hours rep 3

description: Treated

value: Male


title: Rat liver HW 3000 TCDD 19 hours rep 3

description: Treated


title: Rat liver HW 3000 TCDD 19 hours rep 4

description: Treated


title: Rat liver HW 1000 TCDD 19 hours rep 3

description: Treated


title: TGFb1_2


title: Rat liver HW 1000 TCDD 19 hours rep 4

description: Treated


title: Rat liver HW 3000 TCDD 19 hours rep 2

description: Treated


title: Rat liver HW 3000 TCDD 19 hours rep 1

description: Treated


title: LPS_IFNg_2


title: BASAL_1


title: TGFb1_1


title: Rat liver HW 10 TCDD 19 hours rep 2

description: Treated


title: BASAL_2


title: Rat liver HW 10 TCDD 19 hours rep 1

description: Treated


title: LPS_IFNg_1


title: Rat liver HW 100 TCDD 19 hours rep 3

description: Treated


title: Rat liver HW 1 TCDD 19 hours rep 4

description: Treated

source_name: liver, Han/Wistar, 1 TCDD, 19 hour exposure

value: 1 ug/kg TCDD


title: Rat liver HW 1000 TCDD 19 hours rep 1

description: Treated


title: Recombinant 10-157

city: St. Louis

first: Adam

middle: F

last: Allred

state: MO

address: 660 S. Euclid

institute: Washington University in St. Louis, School of Medicine

description: hybridization of infected culture for use in validating VIPR HMM

hyb_protocol: 70 degree incubation for 12 hours

scan_protocol: scanned using GenePix 4000B scanner

data_processing: None. Regarding the submission of raw (not normalized) data, the microarray data provided represents an unconventional use of microarrays as a diagnostic tool as opposed to the conventional use of microarrays to study gene expression patterns. Each software tool that has been developed to analyze diagnostic microarray data employs its own normalization method. Thus, the standard input to these programs is non-normalized data which is then independently processed by whatever software tool is chosen.

organism:
Chlorocebus aethiops
Flavivirus

source_name: infected culture

label_protocol: amino-allyl Cy3 dye coupled to cDNA

extract_protocol: RNA extracted using Trizol extraction protocol

tag: cell line

value: Vero

tag: infection

value: YF/SLE

tag: purpose

value: Validation


title: Rat liver HW 100 TCDD 19 hours rep 2

description: Treated

tag: strain

value: Han/Wistar

tag: age

value: 19 hours


title: Rat liver HW 1000 TCDD 19 hours rep 2

description: Treated

tag: treatment

tag: exposure


title: Recombinant 9-156

value: YF/JE


title: Rat liver HW 100 TCDD 96 hours rep 4

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 96 hour exposure


title: Rat liver HW 1 TCDD 19 hours rep 3

description: Treated


title: Recombinant 9-155


title: Rat liver HW 10 TCDD 19 hours rep 3

description: Treated


title: Rat liver HW 10 TCDD 19 hours rep 1

description: Treated


title: Rat liver HW 1 TCDD 19 hours rep 2

description: Treated


title: Rat liver HW 0.1 TCDD 19 hours rep 4

description: Treated

source_name: liver, Han/Wistar, 0.1 TCDD, 19 hour exposure

value: 0.1 ug/kg TCDD


title: Rat liver HW 1 TCDD 19 hours rep 1

description: Treated

value: Liver


title: Rat liver HW 100 TCDD 19 hours rep 4

description: Treated


title: Rat liver HW 1 TCDD 19 hours rep 3

description: Treated


title: Rat liver HW 10 TCDD 19 hours rep 2

description: Treated


title: Rat liver HW 10 TCDD 19 hours rep 4

description: Treated


title: Recombinant 8-154


title: Recombinant 11-158

value: YF/WN


title: Rat liver HW 100 TCDD 19 hours rep 1

description: Treated


title: Recombinant 8-153


title: Rat liver HW 0.1 TCDD 19 hours rep 3

description: Treated


title: Rat liver HW 1 TCDD 19 hours rep 2

description: Treated


title: Rat liver HW 1 TCDD 19 hours rep 1

description: Treated


title: DENV4-152

description: hybridization of infected culture for use in training VIPR HMM

value: Training


title: Rat liver HW 0.1 TCDD 19 hours rep 4

description: Treated

value: 10-12 weeks


title: Rat liver HW 0.1 TCDD 19 hours rep 2

description: Treated


title: Rat liver HW 0.1 TCDD 19 hours rep 1

description: Treated


title: Rat liver HW 0.1 TCDD 19 hours rep 1

description: Treated


title: Rat liver HW 0.01 TCDD 19 hours rep 4

description: Treated

source_name: liver, Han/Wistar, 0.01 TCDD, 19 hour exposure

value: 0.01 ug/kg TCDD


title: Rat liver HW 0.1 TCDD 19 hours rep 2

description: Treated


title: Rat liver HW 0.01 TCDD 19 hours rep 4

description: Treated


title: Rat liver HW 0.01 TCDD 19 hours rep 3

description: Treated


title: Rat liver HW 0.01 TCDD 19 hours rep 2

description: Treated


title: Rat liver HW 0.01 TCDD 19 hours rep 3

description: Treated


title: Rat liver HW 0.01 TCDD 19 hours rep 1

description: Treated


title: Rat liver HW 0.001 TCDD 19 hours rep 4

description: Treated

source_name: liver, Han/Wistar, 0.001 TCDD, 19 hour exposure

value: 0.001 ug/kg TCDD


title: DENV4-150


title: DENV4-151


title: JEV-147


title: DENV4-149


title: Rat liver HW 0.001 TCDD 19 hours rep 2

description: Treated


title: Rat liver HW 0.001 TCDD 19 hours rep 3

description: Treated


title: Rat liver HW 0.1 TCDD 19 hours rep 3

description: Treated


title: Rat liver HW 0.01 TCDD 19 hours rep 1

description: Treated


title: Rat liver HW 0.01 TCDD 19 hours rep 2

description: Treated


title: DENV4-148


title: JEV-146


title: JEV-145


title: Rat liver HW 0.001 TCDD 19 hours rep 4

description: Treated


title: Rat liver HW 1 TCDD 19 hours rep 4

description: Treated


title: Recombinant 5-143

organism:
Chlorocebus aethiops
Alphavirus

value: SIN/SAEEE


title: Rat liver HW 0.001 TCDD 19 hours rep 3

description: Treated


title: Rat liver HW Corn oil 19 hours rep 4

description: Control

source_name: liver, Han/Wistar, Corn oil treated, 19 hour exposure

value: Corn Oil vehicle


title: Rat liver HW Corn oil 19 hours rep 3

description: Control

value: Male


title: Rat liver HW Corn oil 19 hours rep 5

description: Control


title: Rat liver HW Corn oil 19 hours rep 2

description: Control


title: Rat liver HW 0.001 TCDD 19 hours rep 1

description: Treated


title: Rat liver HW 0.001 TCDD 19 hours rep 2

description: Treated


title: Rat liver HW Corn oil 19 hours rep 6

description: Control


title: Rat liver HW Corn oil 19 hours rep 7

description: Control


title: Rat liver HW Corn oil 19 hours rep 1

description: Control


title: Rat liver HW 100 TCDD 10 hours rep 3

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 10 hour exposure

value: 100 ug/kg TCDD

value: 10 hours


title: Rat liver HW 100 TCDD 10 hours rep 4

description: Treated


title: Recombinant 7-140

value: Vero

value: VEE/CHIK


title: Recombinant 4-142

value: Validation


title: Rat liver HW Corn oil 19 hours rep 7

description: Control

value: Han/Wistar

value: 19 hours


title: Rat liver HW Corn oil 19 hours rep 6

description: Control


title: Rat liver HW 0.001 TCDD 19 hours rep 1

description: Treated


title: Rat liver HW 100 TCDD 10 hours rep 2

description: Treated


title: Recombinant 1-141

value: EEE/CHIK


title: JEV-144


title: Rat liver HW 100 TCDD 6 hours rep 4

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 6 hour exposure

value: Liver

value: 6 hours


title: Recombinant 2-139


title: Rat liver HW Corn oil 19 hours rep 5

description: Control


title: Rat liver HW 100 TCDD 6 hours rep 3

description: Treated


title: Rat liver HW 100 TCDD 6 hours rep 2

description: Treated


title: Rat liver HW Corn oil 19 hours rep 4

description: Control


title: Rat liver HW 100 TCDD 6 hours rep 1

description: Treated


title: Rat liver HW 100 TCDD 3 hours rep 4

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 3 hour exposure

value: 3 hours


title: Recombinant 3-137

value: SIN/CHIK


title: Rat liver HW Corn oil 19 hours rep 3

description: Control

value: 10-12 weeks


title: Rat liver HW 100 TCDD 3 hours rep 3

description: Treated


title: Rat liver HW 100 TCDD 10 hours rep 1

description: Treated


title: Rat liver HW 100 TCDD 3 hours rep 2

description: Treated


title: Recombinant 15-136

value: SIN/EEE/WEE


title: Rat liver HW 100 TCDD 3 hours rep 1

description: Treated


title: Rat liver HW Corn oil 19 hours rep 2

description: Control


title: Rat liver HW 100 TCDD 1.5 hours rep 3

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 1.5 hour exposure

value: 1.5 hours


title: Rat liver HW 100 TCDD 1.5 hours rep 1

description: Treated


title: Rat liver HW Corn oil 1.5 hours rep 3

description: Control

source_name: liver, Han/Wistar, Corn oil treated, 1.5 hour exposure

value: Corn Oil vehicle


title: Recombinant 12-138


title: Rat liver HW Corn oil 1.5 hours rep 2

description: Control

value: Male


title: Rat liver HW 100 TCDD 10 hours rep 3

description: Treated

value: 100 ug/kg TCDD


title: Rat liver HW Corn oil 1.5 hours rep 1

description: Control


title: Rat liver HW 100 TCDD 10 hours rep 2

description: Treated

value: 10 hours


title: Rat liver HW 100 TCDD 19 hours rep 2

description: Treated


title: Rat liver HW 100 TCDD 10 hours rep 1

description: Treated


title: Recombinant 14-133

value: Vero

value: SIN/ZPC


title: Recombinant 6-134

value: SIN/TRD

value: Validation


title: Rat liver HW 100 TCDD 1.5 hours rep 2

description: Treated

value: Han/Wistar


title: Rat liver HW 100 TCDD 10 hours rep 4

description: Treated


title: Recombinant 13-135

value: SIN/NAEEE


title: YFV-131

value: YFV 17D

value: Training


title: YFV-132


title: TGFb1_LPS_IFNg_1

source_name: Primary cortical astrocytes treated with TGF-b1 + LPS + IFNg

value: Primary cortical astrocytes

value: TGF-b1 + LPS + IFNg


title: Rat liver HW 100 TCDD 6 hours rep 2

description: Treated

value: Liver

value: 10-12 weeks

value: 6 hours


title: Rat liver HW 100 TCDD 6 hours rep 3

description: Treated


title: Rat liver HW 100 TCDD 6 hours rep 1

description: Treated


title: Vero-130

organism: Chlorocebus aethiops

source_name: uninfected culture


title: Vero-128


title: Rat liver HW 100 TCDD 3 hours rep 4

description: Treated

value: 3 hours


title: Rat liver HW 100 TCDD 6 hours rep 4

description: Treated

value: Male


title: Bgal dsRNA at T4 hours, biological rep1

first: Sara

last: Cherry

address: 304K Lynch Labs

institute: University of Pennsylvania

description: Gene expression data for basal transcript levels in Drosophila cells

hyb_protocol: The Standard Affymetrix hyb/wash/satining protocolwas used (Protocol FS450 002).

scan_protocol: For Scanning and Image, the GeneChip® Scanner 300) and Affymetrix® GeneChip® Command Console® Software (AGCC) were used.

data_processing: Arrays were analyzed using the Affy (Irizarry et al., 2003) package for R and Microsoft Excel. Background correction was performed with RMA method, data was quantile normalized, only perfect match oligos were used, and probesets were summarized by median polish.  R software  and annotation packages current as of Jan, 2011 were used.

organism: Drosophila melanogaster

source_name: DL1_Bgal dsRNA_mock at T4

label_protocol: Upon fragmentation, 100ng RNA were amplified with the Ovation RNA Amplification System v2 (NuGen), Encore Biotin Module (NuGen) was used for labeling.

growth_protocol: 3 million Drosophila cells (DL1) were treated with 4 ug Bgal dsRNA and incubated for 3 days as described in (Cherry et al. 2005), then either mock-treated or infected with VSV

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

treatment_protocol: Cells were either mock infected or infected with VSV (MOI 10) for 4 hours.

value: Uninfected (mock)


title: Bgal dsRNA at T4 hours, biological rep2


title: Cdk9 dsRNA and VSV infection at T4 hours_biological rep1

description: Gene expression data for transcript levels in Drosophila cells upon VSV infection and Cdk9 dsRNA treatment for 4 hours

data_processing: Arrays were analyzed using the Affy (Irizarry et al., 2003) and limma packages (Smyth, 2004) for R and Microsoft Excel. We calculated fold changes relative to uninfected controls and considered significant genes with at least a 2.8 fold change.

source_name: Drosophila cells treated with Cdk9 dsRNA and infected with VSV at T4 hours, biological rep1

growth_protocol: 3 million Drosophila cells (DL1) were treated with 4 ug Bgal or Cdk9 dsRNA and incubated for 3 days as described in (Cherry et al. 2005), then infected with VSV

treatment_protocol: Cells were infected with VSV (MOI 10) for 4 hours.

value: Cdk9 dsRNA

value: VSV


title: Rat liver HW 100 TCDD 3 hours rep 2

description: Treated

value: 100 ug/kg TCDD


title: Rat liver HW 100 TCDD 3 hours rep 3

description: Treated


title: Bgal dsRNA and VSV infection at T4 hours, biological rep1

description: Gene expression data for transcript levels in Drosophila cells upon VSV infection for 4 hours

source_name: DL1_Bgal dsRNA_VSV at T4

value: VSV (MOI 10) for 4 hours


title: YFV-126

value: Vero


title: Vero-127

value: Validation


title: Bgal dsRNA and VSV infection at T4 hours, biological rep2


title: Cdk9 dsRNA and VSV infection at T4 hours_biological rep2

source_name: Drosophila cells treated with Cdk9 dsRNA and infected with VSV at T4 hours, biological rep2


title: Vero-129


title: Bgal dsRNA and VSV infection at T4 hours_biological rep2

description: Gene expression data for transcript levels in Drosophila cells infected with VSV for 4 hours

source_name: Drosophila cells treated with Bgal dsRNA and infected with VSV at T4 hours, biological rep2

value: Bgal dsRNA


title: YFV-125

source_name: infected culture

value: YFV 17D


title: Bgal dsRNA and VSV infection at T4 hours_biological rep1

source_name: Drosophila cells treated with Bgal dsRNA and infected with VSV at T4 hours, biological rep1


title: MCC, metastatic, tumor MetMCC603, renormalized

city: Ann Arbor

first: Paul

last: Harms

address: 1301 Catherine

department: Pathology

institute: University of Michigan

description: gene expression data from Merkel cell carcinoma, metastatic

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader

data_processing: Data was analyzed using the limma and affy bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC603

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

treatment_protocol: All tumor tissue was procured from the University of Michigan Hospitals Cutaneous Surgery and Oncology Program.  At time of collection, tumor tissue was flash-frozen in liquid nitrogen and stored at -80oC until RNA extraction.  Biopsies of normal skin were flash-frozen at the time of collection and stored at -80oC until time of extraction.

tag: normal or tumor

value: tumor

value: Merkel cell carcinoma

tag: metastasis, primary, or cell line

value: metastatic tumor

tag: merkel cell polyomavirus status (dna and rna)

value: negative


title: MCC, metastatic, tumor MetMCC624, renormalized

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC624


title: MCC, metastatic, tumor MetMCC614, renormalized

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC614

value: positive


title: WNV-123

value: WNV NY99

value: Training


title: Rat liver HW 100 TCDD 3 hours rep 1

description: Treated

value: Male

value: Liver

value: Han/Wistar

value: 10-12 weeks

value: 3 hours


title: MCC, primary, tumor MCC623, renormalized

description: gene expression data from Merkel cell carcinoma, primary

source_name: Merkel cell carcinoma, primary, tumor MCC623

value: primary tumor


title: Recombinant 10-124

value: Vero

value: YF/SLE


title: MCC, metastatic, tumor MetMCC599, renormalized

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC599


title: Gene expression in gastric epithelial cells: control induction +, 24 h

city: Tokyo

first: Yumiko

last: FUJII

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

department: Depertment of Microbiology, Graduate School of Medicine

country: Japan

institute: University of Tokyo

description: Gene expression data in MKN28 (tet-off) cells cultured in the absence of doxycycline.

hyb_protocol: Array hybridization was performed as described previously (Ishii et al., Genomics:136-143, 2000).

scan_protocol: Array scanning was performed as described previously (Ishii et al., Genomics:136-143, 2000).

data_processing: Microarray Suite software 5.0 (Affymetrix) was used to calculate the average differentiation (AD) for each gene probe set, which was shown as an intensity value of the gene expression (Ishii et al., Genomics:136-143, 2000).

source_name: MKN28 (tet-off) cells, doxycycline -, 24 h

label_protocol: Double-stranded cDNA was synthesized with the SuperScript Choice system (GIBCO) and T7-(dT) 24 Primer (GE Amersham) from the total RNA. In vitro transcription was performed to produce biotin-labeld cRNA by using a BioArray HighYield RNA Transcription Labeling Kit (Affymetrix) according to the manufacturer's instructions (Ishii et al., Genomics:136-143, 2000).

growth_protocol: MKN28 (tet-off) cells were cultured in RPMI 1640 medium (Nissui PharmaCeutical Co.) supplemented with 10% fetal bovine serum and 1 μg/ml doxycycline. Cells were grown in a humidified atomosphere with 5% CO2 at 37°C.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen).

treatment_protocol: MKN28 (tet-off) cells, which are able to regulate the expression of a target gene using the Tet-Off System (Clontech), were established from MKN28 human gastric epithelial cells. MKN28 (tet-off) cells were cultured in the absence of Doxycycline (Clontech), a tetracycline analog, for 24 h before harvest (induction +).

tag: cell type

value: gastric epithelial cells

tag: transgene

value: pTet-Off

tag: expression


title: Rat liver HW 100 TCDD 1.5 hours rep 3

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 1.5 hour exposure

tag: gender

value: 100 ug/kg TCDD

value: 1.5 hours


title: WNV-122


title: MCC, primary, tumor MCC611, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC611

value: tumor

value: Merkel cell carcinoma


title: Gene expression in gastric epithelial cells: control induction -, 24 h

description: Gene expression data in MKN28 (tet-off) cells cultured in the presence of doxycycline.

source_name: MKN28 (tet-off) cells, doxycycline +, 24 h

treatment_protocol: MKN28 (tet-off) cells, which are able to regulate the expression of a target gene using the Tet-Off System (Clontech), were established from MKN28 human gastric epithelial cells. MKN28 (tet-off) cells were cultured in the presence of Doxycycline (Clontech), a tetracycline analog, for 24 h before harvest (induction -).


title: Rat liver HW 100 TCDD 1.5 hours rep 2

description: Treated


title: MCC, cell line MCC21, renormalized

description: gene expression data from Merkel cell carcinoma, cell line

source_name: Merkel cell carcinoma, cell line MCC21

value: cell line

value: not done


title: WNV-121

value: WNV NY99

value: Training


title: Rat liver HW 100 TCDD 1.5 hours rep 1

description: Treated

value: Male

value: Liver


title: MCC, primary, tumor MCC622, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC622

value: positive


title: MCC, cell line MCC565, renormalized

source_name: Merkel cell carcinoma, cell line MCC565


title: MCC, primary, tumor MCC601, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC601

value: negative


title: Rat liver HW Corn oil 1.5 hours rep 3

description: Control

source_name: liver, Han/Wistar, Corn oil treated, 1.5 hour exposure

value: Han/Wistar

value: 10-12 weeks

value: Corn Oil vehicle


title: MCC, cell line MCC19, renormalized

source_name: Merkel cell carcinoma, cell line MCC19


title: MCC, cell line MCC13, renormalized

source_name: Merkel cell carcinoma, cell line MCC13


title: WNV-119

source_name: infected culture

value: Vero

value: Validation


title: SLEV-118

value: SLEV CorAn9124


title: Rat liver HW Corn oil 1.5 hours rep 2

description: Control

value: 1.5 hours


title: Rat liver HW Corn oil 1.5 hours rep 1

description: Control


title: MCC, primary, tumor MCC521, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC521

value: tumor

value: primary tumor


title: WNV-120


title: Recombinant 11-117

value: YF/WN


title: MCC, primary, tumor MCC304, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC304

value: Merkel cell carcinoma

value: insufficient DNA


title: MCC, primary, tumor MCC592, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC592


title: MCC, metastatic, tumor MetMCC564, renormalized

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC564

value: metastatic tumor


title: SLEV-116

value: Training


title: MCC, metastatic, tumor MetMCC591, renormalized

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC591


title: MCC, primary, tumor MCC529, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC529


title: MCC, primary, tumor MCC571, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC571


title: MCC, primary, tumor MCC506, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC506


title: MCC, primary, tumor MCC582, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC582


title: MCC, primary, tumor MCC569, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC569


title: MCC, primary, tumor MCC576, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC576


title: MCC, primary, tumor MCC470, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC470


title: SLEV-113


title: MPX_B_96h

city: Varese (VA)

first: Marco

last: Fabbri

address: via dunant 5

country: Italy

institute: Università dell'Insubria

description: Gene expression after treatment with 5 µM mipafox

hyb_protocol: standard Agilent protocol

scan_protocol: Scanned with the Agilent G2565BA Microarray Scanner (Agilent)

data_processing: The fluorescence intensities on scanned images were extracted and by Agilent Feature Extraction Software (v10.5.1.1). Data preprocessing was performed with the Agi4x44PreProcess R package using quantile normalization and quality filtering.

source_name: hNT2 differentiation in presence of mipafox

label_protocol: standard Agilent protocol

growth_protocol: Undifferentiated hNT2 cells were cultured in 75 cm2 flasks at the density of 3 x 10 6 cells with 5% heat-inactivated foetal bovine serum (FBS) plus 50 U/ml penicillin and 100 µg/ml streptomycin in Opti-MEM media. After 24 hours and for initiating differentiation, a differentiation medium with 10 µM retinoic acid, 10% of FBS and antibiotics in DMEM-Glutamax was applied during 4 days. The medium was replaced at the beginning of day 3.

extract_protocol: RNA from hNT2 cells previously was purified using the RNeasy Plus kit (Qiagen, Germantown, MD, USA).

treatment_protocol: Paraoxon (1 µM) and mipafox (5 µM) were applied to cells freshly dissolved in the differentiation medium.

value: 5 µM mipafox


title: MPX_A_96h


title: SLEV-115


title: MCC, primary, tumor MCC412, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC412

value: positive


title: SLEV-114


title: MPX_C_96h


title: MCC, primary, tumor MCC439, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC439

value: negative


title: YFV-106

value: YFV 17D


title: MCC, primary, tumor MCC274, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC274


title: PXN_B_96h

description: Gene expression after treatment with 1 µM paraoxon

source_name: hNT2 differentiation in presence of paraoxon

value: 1 µM paraoxon


title: PXN_C_96h


title: MCC, primary, tumor MCC345, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC345


title: MCC, primary, tumor MCC437, renormalized

source_name: Merkel cell carcinoma, primary, tumor MCC437


title: JEV-108

source_name: infected culture


title: MCC, metastatic, tumor MetMCC562, renormalized

source_name: Merkel cell carcinoma, metastatic, tumor MetMCC562


title: PXN_A_96h


title: MCC, metastatic, tumor MetMCC456, renormalized

source_name: Merkel cell carcinoma, metastatic tumor MetMCC456