title: Group1_100R_8

description: biopsied 24 hours after exposure


title: Chlamydomonas sulfur stress 24h rep6

status: Public on Oct 19 2011

type: RNA

city: Bielefeld

first: Jörg

last: Toepel

address: Universitätsstrasse 27

department: Biology

country: Germany

institute: University of Bielefeld

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

scan_protocol: Scanned on an Agilent scanner. Images were quantified using Agilent Feature Extraction Software (10.7.3.1; Agilent).

data_processing: Agilent Feature Extraction Software (10.7.3.1) was used for background subtraction and LOWESS normalization.

molecule: total RNA

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas reinhardtii

label_protocol: 1 µg of total RNA were labeld according to the agilent quick amplification labeling kit

growth_protocol: TAP media with or without sulfur

extract_protocol: Total RNA extracted using Phenol Chloroform extraction

tag: strain

value: wt cc3491

tag: time (h)


title: Chlamydomonas sulfur stress label1


title: Breast tumor from patient P_48 (methylation data)

type: genomic

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

description: no additional information

hyb_protocol: DNA samples were hybridized onto the HumanMethylation27 BeadChips during 16 hours at 48°C. Unhybridized and non-specifically hybridized DNA were washed from the BeadChips, according to the Infinium® Methylation Manual Protocol (Illumina, San Diego, USA). Labelled nucleotides were added to extend the primers hybridized to the DNA and primers were stained according to the Infinium® Methylation Manual Protocol (Illumina, San Diego, USA).

scan_protocol: The BeadChips were scanned with the Illumina BeadArrayTM Reader.

data_processing:
Data analysis was performed with the Methylation module of the Genome Studio software provided by Illumina using default parameters.

Average beta value is defined as the ratio of signal from a methylated probe (C not converted to T) relative to the sum of both methylated (C not converted to T) and unmethylated probes (C bisulfite-converted to T) (? value=C/[(T+C)+100]

label: biotin and DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Breast tumor

label_protocol: Please see hyb protocol (since labeling occurs AFTER hybridization).

extract_protocol: Genomic DNA from frozen samples was extracted from twenty 10-um sections using the Qiagen-DNeasy Blood &Tissue Kit according to the supplierâ??s instructions (Qiagen, Hilden, Germany). This included a proteinase K digestion at 55Â°C overnight. DNA was quantitated with the NanoDropÂ® ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

tag: quality control

tag: methylation barcode

tag: subtypeihc

value: LumB

tag: grade

tag: node

tag: sizebin

tag: agebin

tag: er

tag: subtypege


title: Breast tumor from patient P_40 (methylation data)

description: no additional information


title: Group1_100R_4

city: Bethesda

first: Atsushi

last: Terunuma

state: MD

address: 37 Convent Drive, 37/3050

department: Dermatology Branch

country: USA

institute: National Cancer Institute

description: biopsied 24 hours after exposure

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: GC-RMA

label: biotin

source_name: skin treated with 100 J/m2 ssR

label_protocol: IVT Labeling Kit (Affymetrix)

extract_protocol: RNeasy (Qiagen)

treatment_protocol: 100 J/m2 ssR

tag: gender

value: female

tag: tissue

value: skin


title: Breast tumor from patient P_37 (methylation data)

description: no additional information

value: Basal


title: Breast tumor from patient P_36 (methylation data)

description: no additional information


title: Breast tumor from patient P_4 (methylation data)

description: no additional information


title: KO-IL17 and TNFa treatment replicate-2

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from__KO-IL17 and TNFa treatment replicate-2

hyb_protocol: Samples were hybridized onto Affymetrix mouse 430 2.0 Arrays (Affymetrix) according to manufacturer's recommendations

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Se genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Mus musculus

source_name: KO-IL17 and TNFa treatment replicate-2

label_protocol: RNA targets were prepared as previously described (1) and 15 mg of fragmented and labeled cRNA was subjected to GeneChip hybridization

growth_protocol: Mouse embryo fibroblast (MEF) were isolated from wt and CIKS deficient mice (ko) after 11-14 days and cultured in vitro

extract_protocol: Mouse embryo fibroblasts were lysed in RLT-buffer, assigned a random processing order by treatment, homogenized with Qiashredder, and extracted in a 96-well format as described previously (1). RNA quality was determined using 2100 Bioanalyzer (Agilent Technologies, Santa Clare, CA) using RNA pico kit.

treatment_protocol: The cells were treated in four different ways: 1. no stimulation (ref); 2. Stimulated with IL-17 (17); Stimulated with TNFa (a); stimulated with IL-17 and TNFa (17a). The cells were lysed after 2 hours in RLT buffer.

tag: cell type

value: embryo fibroblast

tag: treatment

value: IL17 and TNFa

tag: genotype variation

value: KO


title: KO-mock treatment replicate-3

description: Gene expression data from__KO-mock treatment replicate-3

source_name: KO-mock treatment replicate-3


title: Breast tumor from patient P_41 (methylation data)

description: no additional information


title: Breast tumor from patient P_39 (methylation data)

description: no additional information


title: KO-mock treatment replicate-1

description: Gene expression data from__KO-mock treatment replicate-1

source_name: KO-mock treatment replicate-1


title: Breast tumor from patient P_35 (methylation data)

description: no additional information


title: Group1_100R_2

description: biopsied 24 hours after exposure


title: KO-mock treatment replicate-2

description: Gene expression data from__KO-mock treatment replicate-2

source_name: KO-mock treatment replicate-2


title: KO-IL17 and TNFa treatment replicate-6

description: Gene expression data from__KO-IL17 and TNFa treatment replicate-6

source_name: KO-IL17 and TNFa treatment replicate-6


title: Breast tumor from patient P_38 (methylation data)

description: no additional information


title: KO-IL17 and TNFa treatment replicate-4

description: Gene expression data from__KO-IL17 and TNFa treatment replicate-4

source_name: KO-IL17 and TNFa treatment replicate-4


title: Breast tumor from patient P_43 (methylation data)

description: no additional information


title: Group1_R_6

description: biopsied 24 hours after exposure

source_name: skin treated with 1 MED ssR

treatment_protocol: 1 MED ssR


title: Group1_R_8

description: biopsied 24 hours after exposure


title: KO-IL17 and TNFa treatment replicate-3

description: Gene expression data from__KO-IL17 and TNFa treatment replicate-3

source_name: KO-IL17 and TNFa treatment replicate-3


title: Group1_R_10

description: biopsied 24 hours after exposure


title: Group1_R_9

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_34 (methylation data)

description: no additional information


title: C57 72 ozone 3

city: Research Triangle Park

first: Steven

middle: R

last: Kleeberger

state: NC

address: 111 TW Alexander Dr., Building 101, MD D-201

institute: National Institute of Environmental Health Sciences, NIH

description: Gene expression data from left lung samples from C57BL/6 male mice exposed to 0.3 ppm O3  for 72 hours

hyb_protocol: A fragmentation buffer (250mM Tris acetate pH 8.1, 150 mM MgOAc, 500mM KOAc) was used to fragment 15µg of cRNA.  The fragmented cRNA was then hybridized to GeneChips (Affymetrix Mouse Genome 430A 2.0).

scan_protocol: Scanned on an Affymetrix scanner.

data_processing: RMA Express, Visual data mining and statistical analysis

label: Biotin

label_protocol: Double stranded cDNA was synthesized from 4µg of total RNA using the GeneChip Expression 3’ amplification reagents one-cycle cDNA synthesis kit (Affymetrix).  The resultant double-stranded cDNA was column-purified using the GeneChip Sample Cleanup Module.  Biotinylated cRNA was synthesized from the double-stranded cDNA by in vitro transcription (IVT) using the GeneChip Expression 3’ amplification reagents for IVT labeling (Affymetrix), and was subsequently purified by column purification with the GeneChip Sample Cleanup Module (Affymetrix), and quantified.  Quality of biotinylated cRNAs was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100.

growth_protocol: We provided mice with water and pelleted open-formula rodent diet NIH-31 (Zeigler Brothers, Gardners, PA) ad libitum.  All experimental procedures were conducted in accordance with approved National Institutes of Health Humane Care and Use of Laboratory Animals guidelines and the American Physiological Society’s “Guiding Principles in the Care and Use of Animals.”  Animals were treated humanely and with regard for alleviation of suffering.

extract_protocol: Left lobes of mouse lung tissue were harvested, flash frozen in liquid nitrogen, and stored at -80oC.  For RNA extraction, the lung tissue was homogenized in 2ml Trizol (Invitrogen, Calsbad, CA) with a Tekmar Tissumizer and saw-tooth generator.  One ml of homogenate was subsequently processed according to the manufacturer’s (Invitrogen) protocol with the following minor modifications.  Two µl of 5 mg/ml glycogen was used as a carrier for the isopropanol precipitation, duration of the isopropanol precipitation was increased to overnight, and all centrifugation times were increased to 15 minutes.  RNA pellets were resuspended in nuclease-free water.  RNA quality was tested using a Beckman DU680 spectrophotometer, and quality assessment was determined by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100.  A Qiagen RNeasy total RNA cleanup protocol was subsequently performed followed by re-quantitation by spectophotometry.

treatment_protocol: Mice were placed in individual stainless-steel wire cages within a Hazelton 1000 chamber (Lab Products, Maywood, NJ) equipped with a charcoal and high-efficiency particulate air–filtered air supply.  Mice were exposed to 0.3 ppm O3 or filtered air for 24, 48 or 72 hr (23.5 hr/day) as described previously (Cho et al, 2007).

tag: age

value: 6-8 weeks

tag: Sex

value: Male

value: Left lung

tag: supplier

value: Jackson Labs, Bar Harbor, ME

tag: exposure time

value: 72 hours

tag: agent

value: ozone

tag: exposure dose

value: 0.3 ppm O3

tag: test article cas no


title: Group1_R_2

description: biopsied 24 hours after exposure


title: Breast tumor from patient P_33 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode

tag: subtypeihc

tag: grade

tag: node


title: Group1_R_5

description: biopsied 24 hours after exposure

tag: gender


title: KO-TNFa treatment replicate-6

description: Gene expression data from__KO-TNFa treatment replicate-6

source_name: KO-TNFa treatment replicate-6

value: TNFa


title: KO-TNFa treatment replicate-3

description: Gene expression data from__KO-TNFa treatment replicate-3

source_name: KO-TNFa treatment replicate-3


title: KO-TNFa treatment replicate-4

description: Gene expression data from__KO-TNFa treatment replicate-4

source_name: KO-TNFa treatment replicate-4


title: Group1_R_7

description: biopsied 24 hours after exposure

value: male

tag: tissue


title: Group1_R_4

description: biopsied 24 hours after exposure


title: KO-IL17 and TNFa treatment replicate-1

description: Gene expression data from__KO-IL17 and TNFa treatment replicate-1

source_name: KO-IL17 and TNFa treatment replicate-1

tag: cell type


title: KO-TNFa treatment replicate-5

description: Gene expression data from__KO-TNFa treatment replicate-5

source_name: KO-TNFa treatment replicate-5

tag: treatment


title: Breast tumor from patient P_32 (methylation data)

description: no additional information

tag: sizebin

tag: agebin

tag: er

tag: subtypege

value: LumA


title: Breast tumor from patient P_31 (methylation data)

description: no additional information

value: LumB


title: Breast tumor from patient P_29 (methylation data)

description: no additional information


title: Group1_LowR_10

description: biopsied 24 hours after exposure

source_name: skin treated with 0.1 MED ssR

treatment_protocol: 0.1 MED ssR

value: female


title: C57 72 ozone 2

tag: strain

tag: genotype variation

tag: age

tag: Sex

tag: supplier

tag: exposure time


title: Breast tumor from patient P_30 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode

tag: subtypeihc


title: C57 72 ozone 1

tag: agent

tag: exposure dose

tag: test article cas no


title: Breast tumor from patient P_3 (methylation data)

description: no additional information

tag: grade

tag: node


title: Breast tumor from patient P_27 (methylation data)

description: no additional information

tag: sizebin

tag: agebin


title: KO-TNFa treatment replicate-2

description: Gene expression data from__KO-TNFa treatment replicate-2

source_name: KO-TNFa treatment replicate-2

tag: cell type

tag: treatment


title: Breast tumor from patient P_28 (methylation data)

description: no additional information

source_name: Breast tumor

tag: er

tag: subtypege


title: B6.IL10 72 O3 3

description: Gene expression data from left lung samples from B6.129P2-Il10tmlCgn/J male mice exposed to 0.3 ppm O3  for 72 hours

tag: strain

tag: genotype variation

tag: age

tag: Sex

tag: tissue


title: Breast tumor from patient P_26 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode

tag: subtypeihc


title: Group1_LowR_6

description: biopsied 24 hours after exposure

tag: gender

value: skin


title: Breast tumor from patient P_25 (methylation data)

description: no additional information

tag: grade


title: Group1_LowR_7

description: biopsied 24 hours after exposure


title: B6.IL10 72 O3 1

tag: supplier

tag: exposure time

tag: agent

tag: exposure dose

tag: test article cas no


title: Group1_LowR_5

description: biopsied 24 hours after exposure


title: Group1_LowR_9

description: biopsied 24 hours after exposure


title: KO-IL17 treatment replicate-4

description: Gene expression data from__KO-IL17 treatment replicate-4

source_name: KO-IL17 treatment replicate-4

tag: cell type

tag: treatment


title: Breast tumor from patient P_23 (methylation data)

description: no additional information

value: Basal

tag: node

tag: sizebin

tag: agebin

tag: er

tag: subtypege


title: Group1_LowR_4

description: biopsied 24 hours after exposure

tag: tissue


title: KO-IL17 treatment replicate-6

description: Gene expression data from__KO-IL17 treatment replicate-6

source_name: KO-IL17 treatment replicate-6

value: embryo fibroblast

tag: genotype variation


title: B6.IL10 48 O3 2

description: Gene expression data from left lung samples from B6.129P2-Il10tmlCgn/J male mice exposed to 0.3 ppm O3  for 48 hours

tag: strain

tag: age

tag: Sex

value: 48 hours


title: B6.IL10 72 O3 2

tag: supplier


title: B6.IL10 48 O3 3

tag: exposure time


title: B6.IL10 48 O3 1

tag: agent


title: Group1_LowR_2

description: biopsied 24 hours after exposure

tag: gender


title: Group1_LowR_8

description: biopsied 24 hours after exposure


title: KO-TNFa treatment replicate-1

description: Gene expression data from__KO-TNFa treatment replicate-1

source_name: KO-TNFa treatment replicate-1

value: KO


title: KO-IL17 treatment replicate-3

description: Gene expression data from__KO-IL17 treatment replicate-3

source_name: KO-IL17 treatment replicate-3


title: KO-IL17 treatment replicate-5

description: Gene expression data from__KO-IL17 treatment replicate-5

source_name: KO-IL17 treatment replicate-5


title: B6.IL10 48 air 2

description: Gene expression data from left lung samples from B6.129P2-Il10tmlCgn/J male mice exposed to 0 ppm O3  for 48 hours

value: 6-8 weeks

value: air

tag: exposure dose

value: 0 ppm O3


title: Breast tumor from patient P_24 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode

tag: subtypeihc

tag: grade


title: KO-IL17 treatment replicate-2

description: Gene expression data from__KO-IL17 treatment replicate-2

source_name: KO-IL17 treatment replicate-2

tag: cell type

tag: treatment


title: Breast tumor from patient P_21 (methylation data)

description: no additional information

tag: node

tag: sizebin

tag: agebin

tag: er

tag: subtypege


title: KO-IL17 treatment replicate-1

description: Gene expression data from__KO-IL17 treatment replicate-1

source_name: KO-IL17 treatment replicate-1

tag: genotype variation


title: HMG20BKD#2

city: Rotterdam

first: Sjaak

last: Philipsen

address: Dr molewaterplein

department: Cell Biology

country: Netherlands

institute: Erasmus MC

description: Gene expression data from Hmg20b knocked down I/11 cells

hyb_protocol: Affy-169 : 300.0 ng at 45 degree_C during 17 hours

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner 3000

data_processing: The data was normalized by Robust Multi-Array average (RMA) algorithm. Intensities of probe sets lower than 30 were reset to 30.The intensity values of individual probe sets in each sample were then displayed as the log 2 of the deviations to the calculated geometric means for that probe sets

label: Biotin-Affy

source_name: Fetal liver

growth_protocol: I/11 erythroid progenitors were cultured in StemPro34 supplemented with stem cell Factor (SCF), Dexamethasone and Erythropoietin.

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

treatment_protocol: To knockdown Hmg20b, TRCN0000081665 (Hmg20b shRNA#1) was used. Three days after transduction the cells were harvested

tag: tissue type

value: Fetal liver

value: I/11 cells

tag: mutation

tag: genetic background

tag: knockdown


title: B6.IL10 48 air 1

tag: strain

tag: age

tag: Sex

value: Male

tag: tissue

value: Left lung

tag: supplier

value: Jackson Labs, Bar Harbor, ME

tag: exposure time

tag: agent

tag: exposure dose


title: Breast tumor from patient P_20 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode

tag: subtypeihc

tag: grade

tag: node

tag: sizebin


title: Breast tumor from patient P_18 (methylation data)

description: no additional information

tag: agebin

tag: er

tag: subtypege


title: C57 48 ozone 3

description: Gene expression data from left lung samples from C57BL/6 male mice exposed to 0.3 ppm O3  for 48 hours

tag: strain

tag: genotype variation

value: ozone

value: 0.3 ppm O3

tag: test article cas no


title: Muscle_AQM_Treatment_3

city: uppsala

first: sudhakar

middle: reddy

last: aare

address: Ing 85, 3 tr, Akademiska sjukhuset

department: neuroscience

country: Sweden

institute: uppsala university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip  Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 800.

organism: Sus scrofa

source_name: treatment exposed to endotoxin-induced sepsis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

extract_protocol: Total RNA was extracted according to the standard Affymetrix protocol including Trizol extraction and Rneasy column cleanup

treatment_protocol: Four female domestic piglets (Sus scrofa, average body weight 25.5 kg) were used in this study. Piglets were immobilized by anesthesia and mechanically ventilated via a tracheotomy for a period of five days. During this study period, the animals were sedated using isoflurane inhalation (Abbott Laboratories, Chicago, Il, USA, 0.8 – 1.3% end-tidal concentration) supplemented by intravenous bolus doses of morphine and ketamine as needed.  Core body temperature (blood) was maintained in the range of 38.5 – 40°C by a servo controlled heating pad.  The animals received intravenous crystalloid fluid (Ringeracetat) to maintain stable blood pressure and urinary output and a glucose infusion (Rehydrex, Fresenius Kabi, Stockholm, Sweden, 25 mg glucose /mL) in the range of 0.5 – 1.5 mg/kg/minute to decrease the effects of catabolism.  Each animal received prophylactic streptomycin 750 mg/d and bensylpenicillin 600 mg/d (Streptocillin Vet, Boeringer-Ingelheim, Hellerup, Denmark). Arterial blood gas analysis as well as electrolytes and blood glucose levels were monitored regularly and kept in the normal range throughout the study period.Endotoxemia was induced by a continuous infusion of Escherichia coli endotoxin, serotype O26:B6 (Sigma Labkemi, Stockholm, Sweden) at 36 µg/kg/h for 1h.

tag: gender

tag: tissue

value: biceps femoris muscle

tag: disease

value: acute quadriplegic myopathy (AQM)

tag: time period

value: 5 days


title: C57 48 air 1

description: Gene expression data from left lung samples from C57BL/6 male mice exposed to 0 ppm O3  for 48 hours

tag: age

tag: Sex

tag: supplier

tag: exposure time

tag: agent

tag: exposure dose


title: C57 48 air 2


title: HMG20BKD#1

tag: tissue type

tag: cell type

tag: mutation

tag: genetic background

tag: knockdown


title: Muscle_AQM_Treatment_1

value: female


title: Muscle_AQM_Treatment_2


title: C57 48 ozone 2

tag: strain

tag: genotype variation


title: C57 48 ozone 1

tag: test article cas no


title: ctrl#1

description: Gene expression data from normal I/11 cells


title: HMG20BKD#3


title: Muscle_AQM_Treatment_4

tag: gender

tag: tissue


title: Breast tumor from patient P_2 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode

tag: subtypeihc

tag: grade

tag: node

tag: sizebin

tag: agebin

tag: er

tag: subtypege


title: ctrl#2

tag: tissue type

tag: cell type

tag: mutation


title: ctrl#3

tag: genetic background


title: Breast tumor from patient P_19 (methylation data)

description: no additional information

value: LumB

value: LumA


title: B6.IL10 24 ozone 3

description: Gene expression data from left lung samples from B6.129P2-Il10tmlCgn/J male mice exposed to 0.3 ppm O3  for 24 hours

tag: strain

tag: genotype variation

tag: age

tag: Sex

tag: supplier

tag: exposure time

value: 24 hours

tag: agent

tag: exposure dose


title: Breast tumor from patient P_17 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode

tag: subtypeihc

tag: grade

tag: node


title: B6.IL10 24 ozone 1

value: 6-8 weeks

tag: tissue

tag: test article cas no


title: NCI-H292-pcDNA_TNF_rep3

city: Krakow

first: Slawomir

last: Golda

address: Gronostajowa 7

department: Faculty of Biochemistry, Biophysics adn Biotechnology

country: Poland

institute: Jagiellonian University

description: Gene expression after 24hr in treated with TNF NCI-H292 control cells

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven (10 rpm). After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B US22502687) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel was set to Green and Green PMT. Two readings were performed: XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: NCI-H292 cells, pcDNA, 24hr, TNF treated, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug cDNA (reversely transcribed from RNA) using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: NCI-H292 cells were cultured in RPMI-1640 medium suplemented with fetal bovine serum to a final concentration of 10%, at 37.0°C in 5% of CO2

extract_protocol: RNA was prepared using the QIAzol Lysis Reagent (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: NCI-H292 cells, control and overexpressing HO-1, after reaching the confluence were treated with TNF (30 ng/ml) dissolved in RPMI 1640 medium deprived of serum.  The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

tag: overexpression

value: control

tag: treatment

value: TNF


title: NCI-H292-pcHO1_TNF_rep3

description: Gene expression after 24hr in treated with TNF NCI-H292 cells overexpressing HO-1

source_name: NCI-H292 cells, pcHO1, 24hr, TNF treated, replicate 3


title: Breast tumor from patient P_16 (methylation data)

description: no additional information

tag: sizebin

tag: agebin

tag: er

tag: subtypege


title: C57 24 ozone 3

description: Gene expression data from left lung samples from C57BL/6 male mice exposed to 0.3 ppm O3  for 24 hours

tag: strain

tag: genotype variation

tag: age

tag: Sex

tag: supplier

tag: exposure time


title: NCI-H292-pcHO1_naive_rep3

description: Gene expression after 24hr in non treated NCI-H292 cells overexpressing HO-1

source_name: NCI-H292 cells, pcHO1, 24hr, no treatment, replicate 3


title: B6.IL10 24 ozone 2

tag: agent

tag: exposure dose


title: Breast tumor from patient P_14 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode

tag: subtypeihc

value: Basal

tag: grade

tag: node


title: Breast tumor from patient P_13 (methylation data)

description: no additional information

tag: sizebin


title: 4h Donor 4

city: London

first: Joseph

middle: J

last: Boyle

address: Du Cane Rd

department: NHLI

country: United Kingdom

institute: Imperial College London

hyb_protocol: Exactly following the Agilent hyb protocol.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software

source_name: Human monocyte-derived macrophages

label_protocol: The Agilent labelling protocol was exactly following the Agilent protocol.

growth_protocol: PBMCs were isolated from normal human donors, using Ficoll-Hypaque density seperation. Monocytes were purified by adherence for 2h at 37C in medium, and then cultured for 18h in Iscove's modified DME supplemented with L-Glu and 10% autologous serum. Monocytes were grown at 10exp5 cells per well in 24-well plates (Nunc). Very strict asepsis was used throughout and reagents were endotoxin-negative on Limulus kit.

extract_protocol: Cells were lysed in RLT Buffer (Qiagen), which is guanidinium, at 1h or 4h after stimulation, rubbed with a fresh syringe plunger (as rubber policeman), frozen in aliquots at -80C until analysis. Aliquots were assessed for RNA integrity using Bioanalyser and amount using Nanodrop. One aliquot was kept for cDNA preparation (Invitrogen Superscript) and qPCR.

treatment_protocol: Cells were then pulsed with vehicle (DMSO) or purified hemin (Sigma-Aldrich) in DMSO (10micromolar final concentration). The stock hemin in DMSO was at 25mM so the DMSO dilution was 1:2500. The hemin was diluted to 100micromolar in 10%AHS-IMDM and then  a further 1:10.

tag: treatment

value: Vehicle

tag: cell type

value: PBMC

tag: time

value: heme


title: 4h Donor 3


title: 1h Donor 3


title: 4h Donor 2


title: 1h Donor 4


title: 4h Donor 1


title: Breast tumor from patient P_126 (methylation data)

description: no additional information

tag: agebin

tag: er

tag: subtypege


title: Breast tumor from patient P_15 (methylation data)

description: no additional information


title: C57 24 ozone 2

tag: strain

tag: genotype variation

tag: age

tag: Sex

value: Male

tag: tissue

value: Left lung

value: Jackson Labs, Bar Harbor, ME

tag: test article cas no


title: NCI-H292-pcDNA_naive_rep3

description: Gene expression after 24hr in non treated NCI-H292 control cells

source_name: NCI-H292 cells, pcDNA, 24hr, no treatment, replicate 3

tag: cell line

tag: overexpression


title: Breast tumor from patient P_129 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode

tag: subtypeihc

tag: grade


title: C57 24 ozone 1

tag: supplier

tag: exposure time

tag: agent

value: ozone

tag: exposure dose

value: 0.3 ppm O3


title: B6.IL10 24 air 1

description: Gene expression data from left lung samples from B6.129P2-Il10tmlCgn/J male mice exposed to 0 ppm O3  for 24 hours

value: air

value: 0 ppm O3


title: 1h Donor 1

tag: treatment

tag: cell type

tag: time


title: 1h Donor 2


title: C57 24 air 2

description: Gene expression data from left lung samples from C57BL/6 male mice exposed to 0 ppm O3  for 24 hours

tag: strain

tag: genotype variation

tag: age


title: Breast tumor from patient P_124 (methylation data)

description: no additional information

tag: node

tag: sizebin

tag: agebin

tag: er

tag: subtypege


title: NCI-H292-pcDNA_naive_rep2

source_name: NCI-H292 cells, pcDNA, 24hr, no treatment, replicate 2

tag: cell line

tag: overexpression


title: NCI-H292-pcHO1_naive_rep2

source_name: NCI-H292 cells, pcHO1, 24hr, no treatment, replicate 2


title: Healthy Old vs Young Replicate 2

city: Miami

first: Lina

middle: A

last: Shehadeh

state: FL

address: 1600 NW 10th Ave

department: Medicine

institute: University of Miami Miller School of Medicine

hyb_protocol: Labeled cDNAs were hybridized to Agilent Whole Rat Genome Array for 17 hours at 60oC according to manufacturer’s instructions.

scan_protocol: The microarrays were scanned at 5 micron resolution using a GenePix 4000B scanner (Axon Instruments at Molecular Devices). The resulting images were analyzed with the software package GenePix Pro 6.0 (Axon Instruments at Molecular Devices).

data_processing: Data extracted from the images were transferred to the software package Acuity 4.0 (Axon Instruments) for normalization and statistical analysis.Each array was normalized for signal intensities across the whole array and locally, using Lowess normalization. Features for further analysis were selected according to the following quality criteria: (1) at least 90% of the pixels in the spot had intensity higher than background plus two standard deviations; (2), there were less than 2% saturated pixels in the spot; (3) signal to noise ratio (defined as ratio of the background subtracted mean pixel intensity to standard deviation of background) was 3 or above for each channel; (4) the spot diameter was between 110 and 150 micron; (5) the regression coefficient of ratios of pixel intensity was 0.6 or above.

organism: Rattus norvegicus

source_name: Iliac Arteries

label_protocol: 10 ug of total RNA were mixed with the 200 pMol of oligo-dT primer. After 10 min incubation at 70oC and 5 min at 4oC, 20 units of Transcriptor reverse transcriptase (Roche, Cat # 3531287001), 10 nMol of each dNTP and 4 nMol of aminoallyl-dUTP (Ambion, Cat # 8439) were added, and this mix was incubated 2 hours at 42oC. After 30 min RNase treatment cDNA was purified using QIAquick PCR purification Kit (Qiagen, Cat # 28106). Amount of cDNA was determined spectrophotometrically, and samples were dried on speedvac. cDNA was resuspended in the carbonate buffer (pH 9.0 – 9.3) and mixed with the Cy3- and Cy5-NHS ethers (Amersham, Cat # PA23001 and PA25001, respectively). After 1 hour incubation in the dark 20 mMol of hydroxylamine were added to quench the reaction, and labeled cDNA was purified using QIAquick PCR purification Kit. Concentration of the labeled cDNA and labeling efficiency were determined spectrophotometrically.

growth_protocol: Rats (young, old, healthy, or injured) were housed under normal conditions until sacrificed.

extract_protocol: To isolate total RNA from the iliac artery samples, 0.3 mL of TRI Reagent (Molecular Research Center Cat #TRI-118) was added per tissue sample. The sample was then macerated using a Kinematica AG Polytron PT-2100 for 1 min. After a 5 min incubation at room temperature 0.2 volumes of chloroform was added and mixed, following by a 3 min incubation at room temperature and 10 min centrifugation at 12,000 g 4oC. The top aqueous layer was transferred to a new tube containing 0.5 volume of isopropanol and 2 to 10 ul of polyacryl carrier (Molecular Recearch Center, Cat #PC152). After mixing, the precipitate containing the total RNA was collected by 15 min of centrifugation at 12,000 g 4oC. The pellet was then washed two times with 70% ethanol. Total RNA was additionally purified with RNeasy Mini Kit (Qiagen, Cat # 74106). Total RNA yield was determined spectrophotometrically.

value: Fisher

tag: post-injury time

value: no injury

value: 22 months

tag: tissue

value: iliac arteries

value: 3 months


title: Breast tumor from patient P_22 (methylation data)

description: no additional information

source_name: Breast tumor

tag: quality control

tag: methylation barcode

tag: subtypeihc

value: LumA

tag: grade


title: NCI-H292-pcDNA_TNF_rep1

source_name: NCI-H292 cells, pcDNA, 24hr, TNF treated, replicate 1

value: control

tag: treatment

value: TNF


title: Breast tumor from patient P_122 (methylation data)

description: no additional information


title: Healthy Old vs Young Replicate 3

tag: strain


title: NCI-H292-pcHO1_TNF_rep2

source_name: NCI-H292 cells, pcHO1, 24hr, TNF treated, replicate 2


title: C57 24 air 1

tag: genotype variation

value: 6-8 weeks

tag: Sex

tag: supplier

tag: exposure time

value: 24 hours

tag: agent

tag: exposure dose


title: NCI-H292-pcHO1_naive_rep1

source_name: NCI-H292 cells, pcHO1, 24hr, no treatment, replicate 1


title: NCI-H292-pcDNA_TNF_rep2

source_name: NCI-H292 cells, pcDNA, 24hr, TNF treated, replicate 2


title: Breast tumor from patient P_123 (methylation data)

description: no additional information

tag: node

tag: sizebin

tag: agebin

tag: er

tag: subtypege


title: 30 Minutes Post-Injury Young vs Young Replicate 3

tag: post-injury time

value: 30 minutes

tag: age

tag: tissue


title: 30 Minutes Post-Injury Young vs Young Replicate 2


title: Breast tumor from patient P_121 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode

tag: subtypeihc

tag: grade


title: Healthy Old vs Young Replicate 1

tag: strain


title: 30 Minutes Post-Injury Young vs Young Replicate 1


title: Sample 10

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

institute: Health Canada

hyb_protocol: Hybridisations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.

scan_protocol: Arrays were scanned at a resolution of 5 mm using an Agilent G2505B scanner.

data_processing: Data were extracted from scanned images using Agilent Feature Extraction software version 10.7.3.1. Median signal intensities were cyclic lowess normalized.  Technical replicates for each miRNA level were averaged using the median.  Data was flagged if the raw signal intensity was less than the mean plus three standard deviations of the negative controls or if the median of the technical replicates was flagged to be in the background.

label: Cyanine 3-pCp

source_name: liver

label_protocol: Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridisation Kit (Agilent Tech, Mississauga, ON, Canada).

extract_protocol: Total RNA containing the small fraction was isolated from each sample using the miRVana miRNA Isolation Kit (Ambion), Streetsville, ON, Canada). Quality was confirmed using the Agilent 2100 Bioanalyzer and RNA Nano 6000 chips.

treatment_protocol: 25-week old male Muta™Mouse (i.e., transgenic mouse strain 40.6) were dosed daily via oral gavage for 28-days with BaP dissolved in olive oil (25, 50 and 75 mg/kg body weight/day) purchased from Sigma-Aldrich (Oakville, ON, Canada). Each dose group contained 5 animals; 5 animals were also dosed with a vehicle (olive oil) control. Following a 3 day expression period after the last treatment, mice were euthanized with isofluorane followed by cervical dislocation. Liver was then excised, flash-frozen in liquid nitrogen, and stored at -80ºC until use.

value: part of liver

tag: gender

value: male

value: 25 weeks

value: transgenic mouse strain 40.6

tag: date of exposure

value: March 2-30

tag: exposure

value: Exposed to 25 mg/kg Bap

tag: time post exposure

value: 3 days


title: Breast tumor from patient P_120 (methylation data)

description: no additional information

tag: node


title: Breast tumor from patient P_12 (methylation data)

description: no additional information

value: LumB

tag: sizebin


title: NCI-H292-pcDNA_naive_rep1

source_name: NCI-H292 cells, pcDNA, 24hr, no treatment, replicate 1

tag: cell line

tag: overexpression

tag: treatment


title: 30 Minutes Post-Injury Old vs Old Replicate 2

value: Fisher

tag: post-injury time

value: 22 months


title: Breast tumor from patient P_118 (methylation data)

description: no additional information

tag: agebin

tag: er

tag: subtypege


title: 30 Minutes Post-Injury Old vs Old Replicate 1

tag: age

tag: tissue

value: iliac arteries


title: NCI-H292-pcHO1_TNF_rep1

source_name: NCI-H292 cells, pcHO1, 24hr, TNF treated, replicate 1


title: Breast tumor from patient P_119 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode

tag: subtypeihc

value: Basal

tag: grade


title: Breast tumor from patient P_116 (methylation data)

description: no additional information


title: Breast tumor from patient P_115 (methylation data)

description: no additional information


title: Sample 8

tag: gender

tag: strain

tag: date of exposure

tag: exposure


title: 30 Minutes Post-Injury Old vs Old Replicate 3


title: Sample 17

value: Exposed to 75 mg/kg Bap

tag: time post exposure


title: Sample 12

hyb_protocol: Agilent Mouse G4122F Microarrays (containing approximately 44,000 probes) were hybridized with 825 ng Cy5-labelled liver RNA and 825 ng Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA), used as a common reference on all arrays.  Arrays were incubated for 17 hours at 65 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.

scan_protocol: Arrays were scanned scanned on an Agilent G2505B scanner. Data were acquired using Agilent Feature Extraction software version 10.7.3.1

data_processing: A reference design was used to analyse gene expression microarray data. The background fluorescence was measured using the (-)3xSLv1 probes; probes with median signal intensities less than the trimmed mean (trim = 5%) plus three trimmed standard deviations of the (-)3xSLv1 probe were flagged as absent (within the background signal). Data were normalized using lowess using the transform.madata function in the maanova library in R.

source_name: Total RNA from mouse lungs labeled with Cyanine-5 (red)

label_protocol: Individual 200 ng aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent, (5184-3523)).

extract_protocol: RNA was isolated using the TRIzol reagent (Invitrogen Canada Inc., Burlington, ON, Canada), and further purified using RNeasy Mini Kits (Qiagen Inc., Mississauga, ON, Canada).  RNA was quantified using UV spectrophotometer, and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).

value: Exposed to 50 mg/kg Bap

value: :3 days

source_name: universal mouse reference total RNA (Catalog #740100; Stratagene, La Jolla, CA, USA)

extract_protocol: purchased from Stratagene

tag: sample type

value: Total RNA derived from 11 mouse cell lines


title: Sample 1

value: Exposed to 0 mg/kg Bap


title: 30 Minutes Post-Injury Old vs Young Replicate 2

value: 30 minutes

value: 3 months


title: Sample 13

value: part of liver

value: male

value: 25 weeks


title: 30 Minutes Post-Injury Old vs Young Replicate 3


title: 30 Minutes Post-Injury Old vs Young Replicate 1


title: Breast tumor from patient P_113 (methylation data)

description: no additional information

tag: node

tag: sizebin


title: Sample 2

value: transgenic mouse strain 40.6

value: March 2-30


title: B6.IL10 24 air 2

tag: genotype variation

value: 6-8 weeks

tag: Sex

value: Male

value: Left lung

tag: supplier

value: Jackson Labs, Bar Harbor, ME

tag: exposure time

value: 24 hours

tag: agent

value: air

tag: exposure dose

value: 0 ppm O3


title: Sample 14

tag: tissue

tag: age

value: Exposed to 50 mg/kg Bap

value: 3 days


title: Sample 7

value: Exposed to 25 mg/kg Bap


title: Breast tumor from patient P_117 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode

tag: subtypeihc

value: Basal

tag: grade

tag: agebin

tag: er

tag: subtypege


title: Sample 3

tag: gender

tag: strain

tag: date of exposure

tag: exposure

value: Exposed to 0 mg/kg Bap

tag: time post exposure

value: :3 days

tag: sample type

value: Total RNA derived from 11 mouse cell lines


title: Sample 19

value: part of liver

value: male

value: 25 weeks

value: Exposed to 75 mg/kg Bap


title: Sample 4

value: transgenic mouse strain 40.6

value: March 2-30


title: Sample 7


title: 7 Days Post-Injury Old vs Young Replicate 3

value: Fisher

tag: post-injury time

value: 7 days

value: 22 months

value: iliac arteries

value: 3 months


title: Sample 20

value: 3 days


title: Breast tumor from patient P_112 (methylation data)

description: no additional information

tag: node

tag: sizebin


title: Sample 20

tag: tissue

tag: age


title: Sample 19


title: 7 Days Post-Injury Old vs Young Replicate 1


title: 7 Days Post-Injury Old vs Young Replicate 4


title: Sample 6

value: Exposed to 25 mg/kg Bap


title: 7 Days Post-Injury Old vs Young Replicate 2


title: Breast tumor from patient P_11 (methylation data)

description: no additional information

tag: quality control

tag: methylation barcode

value: Basal


title: Breast tumor from patient P_110 (methylation data)

description: no additional information

tag: subtypeihc

value: LumB

tag: grade


title: Sample 16

value: :3 days


title: Sample 15

value: Exposed to 50 mg/kg Bap


title: Sample 11

value: part of liver


title: Sample 18

value: male


title: Sample 11

value: 25 weeks

value: Total RNA derived from 11 mouse cell lines


title: 3 Days Post-Injury Old vs Young Replicate 2


title: 3 Days Post-Injury Old vs Young Replicate 3


title: Sample 1

value: transgenic mouse strain 40.6

value: Exposed to 0 mg/kg Bap


title: Sample 10

value: March 2-30


title: Sample 16

value: Exposed to 75 mg/kg Bap


title: Breast tumor from patient P_108 (methylation data)

description: no additional information

tag: agebin

tag: er


title: Sample 13

tag: gender


title: Breast tumor from patient P_107 (methylation data)

description: no additional information

tag: subtypege

value: LumA


title: 3 Days Post-Injury Old vs Young Replicate 4

tag: strain

value: Fisher

value: 22 months

value: iliac arteries


title: Breast tumor from patient P_125 (methylation data)

description: no additional information


title: Slide 176566

city: Jena

first: Akos

middle: T

last: Kovacs

address: Neugasse 23

department: Institute of Microbiology

institute: Friedrich Schiller University of Jena

description:
Comparison of control non-treated and chitosan-A-treated B. cereus cells.

Net{A} is the raw signal of channel A minus the local corner background signal of channel A.
Net{B} is the raw signal of channel B minus the local corner background signal of channel B.

hyb_protocol: The protocol was performed as described in Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 (PMID: 17183215).

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

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (den Hengst et al J. Biol. Chem. 280:34332-34342; PMID: 16040604). Prior to analysis, automatically and manually flagged spots and spots with very low background-subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Bacillus cereus

source_name: untreated cells

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

growth_protocol: B. cereus grown in Iso Sensitest Broth buffered to pH 6 with 100 mM MES.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Lulko, et. al. J. Mol. Microbiol. Biotechnol. 12:82-95 (PMID: 17183215)). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

treatment_protocol: 50mg/mL chitosan added at mid-log growth phase, and cells harvested after 30 min incubation.

tag: treatment

source_name: chitosan-A-treated cells

value: chitosan A


title: Slide 176564


title: Breast tumor from patient P_109 (methylation data)

description: no additional information


title: Sample 9

tag: date of exposure

tag: exposure

value: Exposed to 25 mg/kg Bap

tag: time post exposure

value: 3 days


title: 3 Days Post-Injury Old vs Young Replicate 1

tag: post-injury time

value: 3 months


title: Sample 12

value: Exposed to 50 mg/kg Bap


title: Sample 18

value: part of liver

value: :3 days

tag: sample type


title: Sample 14

tag: tissue

value: male

value: 25 weeks


title: Sample 8

tag: age

value: transgenic mouse strain 40.6

value: Total RNA derived from 11 mouse cell lines


title: Breast tumor from patient P_103 (methylation data)

description: no additional information

tag: quality control

value: Basal

tag: node

tag: sizebin


title: Sample 6

value: March 2-30


title: Slide 176562


title: Breast tumor from patient P_102 (methylation data)

description: no additional information

tag: methylation barcode

tag: subtypeihc

tag: grade


title: Slide 176565

description:
Comparison of control non-treated and chitosan-B-treated B. cereus cells.

Net{A} is the raw signal of channel A minus the local corner background signal of channel A.
Net{B} is the raw signal of channel B minus the local corner background signal of channel B.

source_name: chitosan-B-treated cells

value: chitosan B


title: Breast tumor from patient P_106 (methylation data)

description: no additional information

value: LumA

tag: agebin

tag: er


title: Sample 3

tag: gender

tag: strain

value: Exposed to 0 mg/kg Bap


title: Breast tumor from patient P_104 (methylation data)

description: no additional information

tag: subtypege


title: Slide 176827

tag: treatment


title: Sample 5

tag: date of exposure

tag: exposure

tag: time post exposure


title: Breast tumor from patient P_101 (methylation data)

description: no additional information


title: Slide 176826


title: Sample 15

tag: tissue

tag: sample type


title: Sample 9

tag: age


title: Breast tumor from patient P_105 (methylation data)

description: no additional information

tag: quality control

tag: node

value: LumB


title: Breast tumor from patient P_1 (methylation data)

description: no additional information

tag: methylation barcode

tag: sizebin


title: Sample 17

value: Exposed to 75 mg/kg Bap


title: Breast tumor from patient P_10 (methylation data)

description: no additional information

tag: subtypeihc

tag: grade


title: FH3

status: Public on Oct 18 2011

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with MBNI re-mapped CDF files, version 9. RMA calculated intensity from MBNI custom annotation with the affy R package.

label_protocol: Standard Affymetrix protocol , 10 ug of Qiagen-purified total RNA.

tag: disease state

value: HLRCC


title: FH2


title: FHN2


title: Sample 4

tag: gender


title: FHN1


title: Day 16 endometria from pregnant heifers high progesterone biol rep 5

first: Jai Prakash

last: Mehta

address: Veterinary Science Center, University College Dublin

department: UCD School of Agriculture, Food Science & Veterinary Medicine

country: Ireland

institute: University College Dublin, Ireland

description: Gene expression data from Day 16 pregnant endometrium with high progesterone concentrations

hyb_protocol: 15 μg of fragmented cRNA were hybridized to the GeneChip® Bovine Genome Array. Each sample was added to a hybridization solution containing 100 mM 2-(N-morpholino) ethanesulfonic acid, 1 M Na+, and 20 mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 μg/ml. Hybridization was performed for 16 h at 45ºC. Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).

scan_protocol: Each array was scanned at 1.56 μm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix).

data_processing: The raw data intensity files were read into R (http://www.r-project.org/) and preprocessed using functions of the Affymetrix and Gene Chip Robust Multi-array Average (GCRMA) packages of the BioConductor project (http://www.bioconductor.org/) (Gentleman et al Genome Biology 2004). Identification of differentially expressed genes from endoemtria between treatments on a given day and within a group across days was achieved using the Limma package employing linear modeling and an empirical Bayes framework to shrink the variance of measurements on each probe set. A modified t-test was carried out and P-values were adjusted for multiple testing using the Benjamini and Hochberg false discovery rate method. Lists of differentially expressed genes were selected on the basis of an adjusted P-value of <0.05.

organism: Bos taurus

source_name: Day 16 in vivo bovine endometrium

label_protocol: cDNA was synthesized from 2 µg of total RNA using One-cycle target labeling and control reagents (Affymetrix, Santa Clara, CA) to produce biotin labeled cRNA.

extract_protocol: Trizol was used to extract total RNA from 300 mg strips of endometira according to manufacturer´s instruction. On-column Dnase digestion and RNA cleanup was performed using hte Qiagen Rneasy mini kit as per manufacturers' instructions.

treatment_protocol: Following estrous synchronization, cross-bred beef heifers (n=210) were randomly assigned to either cyclic control group (n=70) or inseminated. Half of all heifers in both groups received a progesterone releasing intravaginal device (PRID) on day 3 of estrous cycle/early pregnancy to transiently elevate systemic progesterone concentrations in the range of 1 ng/ml. The PRID device remained in situ until the day of slaughter. This resulted in four treatment groups: 1) cyclic heifers normal progesterone (CN), 2) cyclic heifers high progesterone (CH), 3) confirmed pregnant heifers with normal progesterone (PN) and 4) confirmed pregnant heifers with high progesterone (PH). Heifers were randomly assigned to slaughter on either Day 5, 7, 13 or 16 of the estrous cycle/early pregnancy.

tag: time

value: Day 16

value: endometrium

tag: heifer status

value: pregnant

tag: progesterone

value: high progesterone


title: FH5


title: PRCC2_11


title: FH4


title: PRCC2_12


title: Day 16 endometria from pregnant heifers high progesterone biol rep 4


title: Day 16 endometria from pregnant heifers high progesterone biol rep 3


title: Day 16 endometria from pregnant heifers normal progesterone biol rep 2

description: Gene expression data from Day 16 pregnant endometrium with normal progesterone concentrations

value: normal progesterone


title: Day 16 endometria from pregnant heifers high progesterone biol rep 2


title: Day 16 endometria from pregnant heifers normal progesterone biol rep 3


title: Day 16 endometria from pregnant heifers normal progesterone biol rep 5


title: Day 16 endometria from pregnant heifers normal progesterone biol rep 4


title: PRCC2_03


title: PRCC2_10


title: PRCC2_08


title: PRCC2_04


title: FH1


title: PRCC2_09


title: PRCC2_05


title: PRCC2_07


title: PRCC2_06


title: Day 16 endometria from cyclic heifers high progesterone biol rep 5

description: Gene expression data from Day 16 cyclic endometrium with high progesterone concentrations

value: cyclic


title: Day 16 endometria from pregnant heifers normal progesterone biol rep 1


title: Day 16 endometria from cyclic heifers high progesterone biol rep 4


title: PRCC2_02


title: Day 16 endometria from cyclic heifers high progesterone biol rep 1


title: Day 16 endometria from cyclic heifers high progesterone biol rep 2


title: PRCC1_20


title: PRCC1_19


title: PRCC2_01


title: PRCC1_17


title: Day 16 endometria from cyclic heifers normal progesterone biol rep 5

description: Gene expression data from Day 16 cyclic endometrium with normal progesterone concentrations


title: Day 16 endometria from cyclic heifers high progesterone biol rep 3


title: PRCC1_22


title: PRCC1_21


title: Day 16 endometria from cyclic heifers normal progesterone biol rep 3


title: Day 16 endometria from pregnant heifers high progesterone biol rep 1


title: PRCC1_14


title: PRCC1_18


title: Day 16 endometria from cyclic heifers normal progesterone biol rep 2


title: Day 13 endometria from pregnant heifers high progesterone biol rep 2

description: Gene expression data from Day 13 pregnant endometrium with high progesterone concentrations

source_name: Day 13 in vivo bovine endometrium

value: Day 13


title: PRCC1_15


title: Day 16 endometria from cyclic heifers normal progesterone biol rep 4


title: PRCC1_13


title: OrR 3SG ORC2 ChIP 2

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Slides were hybridized to custom Agilent tiling arrays and washed as per Agilent recommendations

scan_protocol: Arrays were scanned on an Agilent scanner per manufacturer's protocol

data_processing: Raw data was median normalized using the Ringo package in R in order to generate .wig files containing smoothed log ratios.

organism: Drosophila melanogaster

source_name: orc2 ChIP DNA from third instar salivary gland from OrR

label_protocol: DNA was labeled using Invitrogen's BioPrime Total for Agilent aCGH labeling kit

growth_protocol: Drosophila were grown on standard cornmeal, molasses agar media.

extract_protocol: Salivary glands were fixed with 2% formaldehyde in EBR medium for 15 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with TBS and flash frozen in liquid nitrogen.  Approximately 200 salivary glands were thawed, pooled, and placed in 0.5 mL of ChIP lysis buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate). The crosslinked chromatin was sheared to an average size of 300-1000 bp by three 12-second pulses using a Branson 250 sonicator. The lysate was then centrifuged to remove cell debris. 50 uL was saved for the input DNA from each sample. The chromatin supernatant was then incubated overnight with 2 uL of antibody at 4C. After incubation with 30 uL protein G Dynabeads beads (Invitrogen) for 2h at 4C, the immune complexes were collected using the Dynal magnetic strip and washed with the following buffers at room temperature for 5 minutes each: 2X ChIP lysis buffer, 2X high salt (500mM NaCl) ChIP lysis buffer, 1X ChIP lysis buffer, 1X TE. The protein-DNA complexes were eluted from the beads in 100 uL ChIP elution buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA/1% SDS) at 65C for 15 min followed by another wash with 150 uL TE/0.67% SDS. Eluates were pooled and incubated at 65C for at least 6 hours. Input DNAs were similarly subject to reversal of crosslinks with 200 µL TE/1% SDS. Samples were treated with 100 ug proteinase K at 37C for 2 hours. DNA samples were phenol chloroform extracted twice and ethanol precipitated.

treatment_protocol: Salivary glands were hand dissected from committed wandering third instar larvae directly into EBR medium with protease inhibitors on ice.  After no more than 30 minutes samples were fixed and processed as described below.

tag: cell type

value: third instar salivary gland

tag: strain

value: OrR (WT)

tag: antibody

value: orc2 (Steve Bell, MIT)

source_name: control IgG pulldown DNA from OrR salivary glands

value: OrR

value: control IgG (upstate 12-370)


title: Day 13 endometria from pregnant heifers high progesterone biol rep 3

tag: tissue


title: Day 13 endometria from pregnant heifers high progesterone biol rep 4


title: Day 13 endometria from pregnant heifers high progesterone biol rep 1


title: PRCC1_16


title: Day 13 endometria from pregnant heifers normal progesterone biol rep 5

description: Gene expression data from Day 13 pregnant endometrium with normal progesterone concentrations


title: PRCC1_12


title: Day 13 endometria from pregnant heifers high progesterone biol rep 5


title: PRCC1_09


title: Day 13 endometria from pregnant heifers normal progesterone biol rep 4


title: PRCC1_10


title: PRCC1_07


title: Day 16 endometria from cyclic heifers normal progesterone biol rep 1


title: PRCC1_06


title: Day 13 endometria from pregnant heifers normal progesterone biol rep 2


title: PRCC1_08


title: PRCC1_11


title: R1-A

city: Houston

first: Thomas

middle: Paul

last: Zwaka

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Illumina Whole-Genome Gene Expression Direct  Hybridization Assay.

scan_protocol: BeadArray Reader with Beadscan software to determine the intensity values for each bead type and creates data files for each channel. GenomeStudio software were used analyzing gene expression data from scanned microarray images collected from BeadArray Reader.

data_processing: Raw data were normalized by quantile normalization method and analyzed by DNASTAR ArrayStar software

source_name: ES cells

label_protocol: Illumina  TotalPrep RNA Amplification Kit (Ambion). Illumina Gene Expression protocols feature a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining

growth_protocol: Standard mouse ES cell culture condition with MEF feeder

extract_protocol: RNeasy kit (Qiagen)

tag: passage

tag: cell line

value: ES


title: PRCC1_04


title: Day 13 endometria from pregnant heifers normal progesterone biol rep 1


title: PRCC1_03


title: PRCC1_05


title: AFF204#21-A

treatment_protocol: Standard mouse ES cell culture condition with MEF feeder


title: PRCC1_02


title: chRCC08

value: Chromophobe


title: Day 13 endometria from pregnant heifers normal progesterone biol rep 3


title: Day 13 endometria from cyclic heifers high progesterone biol rep 5

description: Gene expression data from Day 13 cyclic endometrium with high progesterone concentrations


title: chRCC07


title: chRCC10


title: chRCC06


title: chRCC09


title: chRCC05


title: 2i-RFP-

value: 2i derived ES


title: PRCC1_01


title: chRCC03


title: 2i-RFP+


title: CCRCC08

value: ccRCC


title: chRCC04


title: CCRCC06


title: Rhesus cortex adult 2 (mRNA)

city: shanghai

first: Song

last: Guo

address: 320 Yue Yang Road

country: China

institute: PICB

description: Gene expression of Rhesus cortex adult 2

hyb_protocol: Hybridization to Affymetrix® Human Exon 1.0 ST arrays was carried out following standard Affymetrix protocols.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Prior to expression data analysis, we masked all probes that did not match reference human genomes perfectly (hg18) and did not map to a unique location. To determine whether the signal intensity of a given probe was above the expected level of background noise, we compared the signal intensity for each probe to a distribution of signal intensities of the antigenomic probes with the same GC content. Antigenomic probes are specifically designed by Affymetrix to provide an estimate of the non-specific background hybridization. The probe signal was classified as detected above background if its intensity was larger than the 95% percentile of the background probes with the same GC content. If more than 80% of probes and at least ten probes per transcript were detected, the transcript signal was classified as detected for each sample. To further remove any possible systematic experimental differences between the arrays, we performed a PM-GCBG correction and quantile normalization. Prior to the normalization, all intensities were base-two-logarithm transformed. The intensities of transcripts were summarized by median polish method
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.all.ps

organism: Macaca mulatta

source_name: Dissected Rhesus Macaque post-mortem superior frontal gyrus

label_protocol: Biotinylated cRNA were prepared from 2 microg. total RNA following standard Affymetrix protocols.

extract_protocol: Trizol extraction of total RNA from 100 mg of tissue was performed according to the manufacturer's instructions.

treatment_protocol: All human postmortem brain tissue samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders (NICHDBB)(Baltimore, MD, USA). All subjects were defined as normal controls by forensic pathologists at the NICHDBB. No subjects with prolonged agonal state were used. Chimpanzee samples were obtained from the Yerkes Primate Center (Atlanta, GA, USA), from the Biomedical Primate Research Centre (Rijswijk, Netherlands) and from the Anthropological Institute of the University of Zurich (Switzerland).

value: superior frontal gyrus of the brain


title: chRCC01


title: Day 13 endometria from cyclic heifers high progesterone biol rep 4


title: chRCC02


title: Day 13 endometria from cyclic heifers high progesterone biol rep 3


title: Rhesus cortex adult 1 (mRNA)

description: Gene expression of Rhesus cortex adult 1


title: CCRCC05


title: Day 13 endometria from cyclic heifers high progesterone biol rep 2


title: CCRCC07


title: Day 13 endometria from cyclic heifers normal progesterone biol rep 5

description: Gene expression data from Day 13 cyclic endometrium with normal progesterone concentrations


title: Day 13 endometria from cyclic heifers normal progesterone biol rep 4


title: CCRCC02


title: Chimpanzee cortex adult 5 (mRNA)

description: Gene expression of Chimpanzee cortex adult 5

organism: Pan troglodytes

source_name: Dissected chimpanzee post-mortem superior frontal gyrus


title: Day 13 endometria from cyclic heifers normal progesterone biol rep 2


title: Day 13 endometria from cyclic heifers high progesterone biol rep 1


title: Day 13 endometria from cyclic heifers normal progesterone biol rep 3


title: Chimpanzee cortex adult 4 (mRNA)

description: Gene expression of Chimpanzee cortex adult 4


title: CCRCC04


title: NO8


title: NO7


title: Day 7 endometria from pregnant heifers high progesterone biol rep 5

description: Gene expression data from Day 7 pregnant endometrium with high progesterone concentrations

source_name: Day 7 in vivo bovine endometrium

value: Day 7


title: 3SG orc1 mut CGH rep1

source_name: third instar salivary gland from orc1 mut

extract_protocol: Salivary glands were sonicated in in 0.5 mL of ChIP lysis buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate) and phenol-chloroform extracted and ethanol precipitated.

treatment_protocol: Salivary glands were hand dissected from committed wandering third instar larvae directly into EBR medium.  Immediately before freezing at -80C, EBR was removed. Control channel gDNA was from collection plates of 0-2h staged eggs from WT (OrR) Drosophila

source_name: OrR (WT) embryonic 0-2h diploid gDNA


title: Day 7 endometria from pregnant heifers high progesterone biol rep 4

value: endometrium


title: CCRCC03


title: NO3


title: 3SG orc2 mut (Exel6171Df) CGH

source_name: third instar salivary gland from orc2 mut


title: 3SG orc2 mut (Exel6288Df) CGH


title: NO5


title: Chimpanzee cortex adult 2 (mRNA)

description: Gene expression of Chimpanzee cortex adult 2


title: Chimpanzee cortex adult 3 (mRNA)

description: Gene expression of Chimpanzee cortex adult 3


title: NO4


title: Day 13 endometria from cyclic heifers normal progesterone biol rep 1


title: Chimpanzee cortex adult 1 (mRNA)

description: Gene expression of Chimpanzee cortex adult 1


title: NO2


title: Human cortex adult 4 (mRNA)

description: Gene expression of Human cortex adult 4

source_name: Dissected human post-mortem superior frontal gyrus


title: Day 7 endometria from pregnant heifers high progesterone biol rep 1

value: pregnant


title: H3K27me3 ChIP 3SG OrR [1_1]

source_name: H3K27me3 ChIP DNA from third instar salivary gland from OrR


title: Day 7 endometria from pregnant heifers high progesterone biol rep 3

value: high progesterone


title: NO1


title: Human cortex adult 5 (mRNA)

description: Gene expression of Human cortex adult 5


title: CCRCC01


title: Day 7 endometria from pregnant heifers high progesterone biol rep 2


title: SuUR H3K27me3 ChIP

source_name: H3K27me3 ChIP DNA from third instar salivary gland from SuUR

value: SuUR-

source_name: Input DNA from SuUR salivary glands


title: H3K27me3 ChIP 3SG OrR [1_2]

source_name: Input DNA from OrR salivary glands


title: Human cortex adult 3 (mRNA)

description: Gene expression of Human cortex adult 3


title: OrR 3SG RNAPolII ChIP 1

source_name: RNAPolII ChIP DNA from third instar salivary gland from OrR

value: RNAPolII (Millipore CTD4H8)

source_name: Control IgG pulldown DNA from OrR salivary glands

value: control IgG (Upstate 12-371)


title: SuUR 3SG ORC2 ChIP 2

source_name: orc2 ChIP DNA from third instar salivary gland from SuUR

value: third instar salivary gland

source_name: control IgG pulldown DNA from SuUR salivary glands


title: Day 7 endometria from pregnant heifers normal progesterone biol rep 5

description: Gene expression data from Day 7 pregnant endometrium with normal progesterone concentrations

value: normal progesterone


title: Day 7 endometria from pregnant heifers normal progesterone biol rep 4


title: Human cortex adult 1 (mRNA)

description: Gene expression of Human cortex adult 1


title: Human cortex adult 2 (mRNA)

description: Gene expression of Human cortex adult 2


title: NO6


title: Day 7 endometria from pregnant heifers normal progesterone biol rep 2


title: Day 7 endometria from cyclic heifers normal progesterone biol rep 5

description: Gene expression data from Day 7 cyclic endometrium with normal progesterone concentrations

value: cyclic


title: Triptolide, 6 hours, replicate 1

first: Guo

last: Wei

address: 7 Cambridge Center

institute: Broad Institute or MIT and Harvard

description: Gene expression after treatment

hyb_protocol: Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.

scan_protocol: Scans were performed on Affymetrix scanners.

data_processing: Raw expression values were normalized using Robust Multiarray Averaging (RMA).

source_name: triptolide treated for 6 hours

label_protocol: First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.

growth_protocol: MCF7 cells were cultured with RPMI-1640 media supplemented with 10% FBS, 2 mM glutamine, and 1X penn/strp.

treatment_protocol: Cells were treated with actinomycin D at 2.5 uM or triptolide at 500 nM.

tag: compound

value: Triptolide

value: 6 hours


title: Actinomycin D, 6 hours, replicate 1

description: Gene expression after treatment

source_name: Actinomycin D treated for 6 hours

value: Actinomycin D


title: Triptolide, 6 hours, replicate 2

description: Gene expression after treatment


title: Day 7 endometria from pregnant heifers normal progesterone biol rep 1


title: Day 7 endometria from cyclic heifers high progesterone biol rep 3

description: Gene expression data from Day 7 cyclic endometrium with high progesterone concentrations


title: Day 7 endometria from cyclic heifers high progesterone biol rep 2


title: Triptolide, 4 hours, replicate 1

description: Gene expression after treatment

source_name: triptolide treated for 4 hours

value: 4 hours


title: Triptolide, 2 hours, replicate 2

description: Gene expression after treatment

source_name: triptolide treated for 2 hours

value: 2 hours


title: Day 7 endometria from cyclic heifers normal progesterone biol rep 3

source_name: Day 7 in vivo bovine endometrium


title: Actinomycin D, 6 hours, replicate 2

description: Gene expression after treatment


title: Triptolide, 4 hours, replicate 2

description: Gene expression after treatment


title: Day 7 endometria from cyclic heifers normal progesterone biol rep 4


title: Day 7 endometria from pregnant heifers normal progesterone biol rep 3


title: Actinomycin D, 4 hours, replicate 1

description: Gene expression after treatment

source_name: Actinomycin D treated for 4 hours


title: Day 7 endometria from cyclic heifers normal progesterone biol rep 1


title: Day 7 endometria from cyclic heifers normal progesterone biol rep 2


title: Actinomycin D, 4 hours, replicate 2

description: Gene expression after treatment


title: Triptolide, 2 hours, replicate 1

description: Gene expression after treatment


title: Day 7 endometria from cyclic heifers high progesterone biol rep 5


title: Actinomycin D, 2 hours, replicate 2

description: Gene expression after treatment

source_name: Actinomycin D treated for 2 hours


title: DMSO 6 hours, replicate 2

description: Gene expression after treatment

source_name: Control cells at 6h

value: Control


title: Actinomycin D, 2 hours, replicate 1

description: Gene expression after treatment


title: Day 7 endometria from cyclic heifers high progesterone biol rep 4


title: Day 5 endometria from pregnant heifers high progesterone biol rep 4

description: Gene expression data from Day 5 pregnant endometrium with high progesterone concentrations

source_name: Day 5 in vivo bovine endometrium

value: Day 5


title: Day 5 endometria from pregnant heifers high progesterone biol rep 5


title: Day 5 endometria from pregnant heifers high progesterone biol rep 3


title: DMSO 2 hours, replicate 1

description: Gene expression after treatment

source_name: Control cells at 2h


title: DMSO 2 hours, replicate 2

description: Gene expression after treatment


title: Day 5 endometria from pregnant heifers normal progesterone biol rep 1

description: Gene expression data from Day 5 pregnant endometrium with normal progesterone concentrations


title: Day 5 endometria from pregnant heifers high progesterone biol rep 1


title: NMuMG cells_Halofuginone_8hr_Biological replicate3_tech replicate 3

city: Boston

first: Yana

middle: George

last: Kamberov

address: 77 Ave Louis Pasteur

institute: Harvard University

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
sm9

hyb_protocol: Hybridization at 50°C overnight using the Maui (BioMicro Systems, Inc,  Salt Lake City, UT)  hybridization chamber, non-specific targets were  washed away by 3 washing steps, and the slides were dried by  centrifugation.

scan_protocol: The arrays were scanned by an Axon 4000 scanner (Molecular Devices,  Sunnyvale, CA, USA). The Cy5 fluorescent intensity of each spot was  analyzed by Genepix 4.1 software (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
Quantile-normalization was performed to the probe-level signal using AnyExpress (http://anyexpress.sourceforge.net; PMID: 21410990).
Filtering Details :We removed 7949 (=29922 - 21973) probes whose sequence and annotation information was not available from the manufacturer.

source_name: NMuMG cells, Halofuginone, 8hr

label_protocol: Fluorescent targets were hybridized to the mouse whole genome OneArray (Phalanx Biotech Group, Hsinchu, Taiwan) with Phalanx hybridization buffer.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s protocol.  The extracted RNA was then treated with RQ1-DNAse I (Promega) for 30 min and subsequently extracted with Phenol-Chloroform-Isoamyl Alcohol (Ambion), followed by a Chloroform (Sigma) extraction and precipitated with Ammonium Acetate/Ethanol.

treatment_protocol: NMuMG cells were freshly plated into complete growth media and 45minutes later 10 nM Halofuginone or 10 nM MAZ1310 inactive analog diluted in acidified DMSO was added for 8 hours prior to harvesting.

tag: cell origin

value: normal glandular mammary tissue

tag: morphology

value: epithelial


title: DMSO 4 hours, replicate 2

description: Gene expression after treatment

source_name: Control cells at 4h


title: DMSO 4 hours, replicate 1

description: Gene expression after treatment


title: Day 5 endometria from pregnant heifers normal progesterone biol rep 4

value: endometrium

value: pregnant


title: Day 5 endometria from pregnant heifers normal progesterone biol rep 3


title: Day 5 endometria from pregnant heifers high progesterone biol rep 2

value: high progesterone


title: Day 5 endometria from pregnant heifers normal progesterone biol rep 5


title: DMSO 6 hours, replicate 1

description: Gene expression after treatment


title: NMuMG cells_Halofuginone_8hr_Biological replicate3_tech replicate 2

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
sm8


title: Day 5 endometria from pregnant heifers normal progesterone biol rep 2


title: cl02150831.cel

last: Hill

address: 300 Technology Square

department: Research Business Technology

institute: Pfizer

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: Affymetrix MAS 5.0 algorithm

label_protocol: Affymetrix in-vitro labeling protocol

extract_protocol: RNA was extracted from L4 and L5 rat dorsal root ganglion (DRG)

value: Sprague-Dawley

value: male

tag: procedure

value: Sham

tag: contralateral or ipsilateral

value: c

tag: extract

tag: affy chip


title: NMuMG cells_Halofuginone_8hr_Biological replicate3_tech replicate 1

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
sm7


title: DLD1_shGATA6

city: Tokyo

first: Tetsu

last: Akiyama

address: 1-1-1, Yayoi, Bunkyo-ku

department: Institute of Molecular and Cellular Biosciences

country: Japan

institute: Tokyo University

hyb_protocol: Agilent protocol

scan_protocol: Agilent protocol

data_processing: Data sets were imported into Gene Spring for normalization and statistical analysis.

source_name: DLD1, shRNA targeting GATA6

label_protocol: Agilent protocol

extract_protocol: Total RNA was prepared using Total RNA Isolation (MACHEREY-NAGEL).

value: colorectal cancer cell line DLD1

tag: treatment protocol

value: shRNA targeting GATA6


title: Day 5 endometria from cyclic heifers high progesterone biol rep 5

description: Gene expression data from Day 5 cyclic endometrium with high progesterone concentrations

tag: time

value: cyclic


title: cl02150807.cel

tag: gender

value: SNL


title: NMuMG cells_Halofuginone_8hr_Biological replicate2_tech replicate 3

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
sm6


title: DLD1_shLGR5

source_name: DLD1, shRNA targeting LGR5

value: shRNA targeting LGR5


title: Day 5 endometria from cyclic heifers high progesterone biol rep 3

tag: heifer status

tag: progesterone


title: DLD1_shEmpty

source_name: DLD1, Control shRNA

value: control


title: NMuMG cells_Halofuginone_8hr_Biological replicate2_tech replicate 2

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
sm5


title: cl02150803.cel

tag: strain

value: i


title: cl02150828.cel


title: cl02150821.cel


title: NMuMG cells_Halofuginone_8hr_Biological replicate1_tech replicate 3

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
sm3


title: SuUR 3SG RNAPolII ChIP 1

source_name: RNAPolII ChIP DNA from third instar salivary gland from SuUR

tag: cell type

value: third instar salivary gland

value: SuUR-

tag: antibody

value: RNAPolII (Millipore CTD4H8)

source_name: Control IgG pulldown DNA from SuUR salivary glands

value: control IgG (Upstate 12-371)


title: cl02200802.cel

tag: tissue


title: cl02150814.cel


title: NMuMG cells_Halofuginone_8hr_Biological replicate2_tech replicate 1

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
sm4

value: normal glandular mammary tissue

value: epithelial


title: Day 5 endometria from cyclic heifers high progesterone biol rep 4

value: Day 5

value: endometrium

value: high progesterone


title: cl02150805.cel

value: Sprague-Dawley

value: male


title: cl02200807.cel

value: c


title: cl02200801.cel


title: cl02150823.cel

value: Sham


title: cl02150809.cel

value: SNL


title: cl02150801.cel


title: NMuMG cells_Halofuginone_8hr_Biological replicate1_tech replicate 2

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
sm2


title: 3SG SuUR CGH rep2

source_name: third instar salivary gland from SuUR

source_name: OrR (WT) embryonic 0-2h diploid gDNA

value: OrR (WT)


title: SuUR 3SG ORC2 ChIP 1

source_name: orc2 ChIP DNA from third instar salivary gland from SuUR

value: orc2 (Steve Bell, MIT)

source_name: Input DNA from SuUR salivary glands


title: Day 5 endometria from cyclic heifers high progesterone biol rep 2

value: cyclic


title: cl02200804.cel

value: i


title: OrR 3SG ORC2 ChIP 1

source_name: orc2 ChIP DNA from third instar salivary gland from OrR

value: third instar salivary gland

source_name: Input DNA from OrR salivary glands

value: OrR


title: Day 5 endometria from cyclic heifers normal progesterone biol rep 5

description: Gene expression data from Day 5 cyclic endometrium with normal progesterone concentrations

value: normal progesterone


title: cl02150810.cel


title: 3SG SuUR CGH rep1

value: SuUR-


title: cl02150815.cel


title: Day 5 endometria from cyclic heifers normal progesterone biol rep 3


title: NMuMG cells_MAZ1310_8hr_Biological replicate3_tech replicate 1

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
ctl7

source_name: NMuMG cells, MAZ1310, 8hr

value: normal glandular mammary tissue

value: epithelial


title: Day 5 endometria from cyclic heifers normal progesterone biol rep 4

value: Day 5

value: endometrium


title: cl02150804.cel

value: Sprague-Dawley


title: NMuMG cells_MAZ1310_8hr_Biological replicate3_tech replicate 3

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
ctl9


title: cl02150832.cel

value: male


title: cl02150822.cel

value: c


title: liver_HF_clodronate_pool

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA (v2.24.1) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.

source_name: liver tissue from C57Bl/6J mice fed HFD for 20 weeks, clodronate injection, pool of RNA of 10 mice

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).

growth_protocol: Male C57Bl/6J mice (Charles River, L'Arbresle Cedex, France) were housed 2 per cage in a light-and-temperature controlled facility (lights on 6:30 to 18:30, 21°C).

extract_protocol: Total RNA was prepared from mouse livers using TRIzol reagent, followed by purification of total RNA using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).  For array analyses, equal amounts of RNA per animal was pooled per experimental group to give 4 pooled samples.

treatment_protocol: At the age between 8-12 weeks, mice were fed a low-fat diet (LFD; n = 16) or a high-fat diet (HFD; n = 20) for 20 weeks, providing 10 or 45 energy percent as fat, respectively (D12450B or D12451; Research Diets, New Brunswick, NJ). The lard component in these diets was replaced by palm oil. In the last week of the diet intervention, half of the animals of each diet group received an intraperitoneal injection with clodronate liposomes or PBS twice.

tag: Sex

tag: age

value: 8-12 weeks at beginning of diet intervention


title: NMuMG cells_MAZ1310_8hr_Biological replicate3_tech replicate 2

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
ctl8

tag: cell origin


title: NMuMG cells_Halofuginone_8hr_Biological replicate1_tech replicate 1

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
sm1

tag: morphology


title: NMuMG cells_MAZ1310_8hr_Biological replicate2_tech replicate 3

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
ctl6


title: Control_3_MSRE_rep2

city: Jerusalem

first: Asaf

last: Hellman

address: Hadassah Medical School

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University

description: Hybridized to SNP 6.0

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Affymetrix SNP6 microarrays were processed and scanned according to the manufacturer’s instructions (www.Affymetrix.com). Hybridization intensities were normalized using the dChip software package Build date: Jul 19 2010 (www.dchip.org). Methylation signals, defined as 1-log2 of the ratio between hybridization intensities before/after MSRE treatments were assigned to each one of the 1,461,753 DNA fragments with at least one MSRE site, probed on the Affymetrix SNP6 microarray.
The matrix file contain 20 columns. Each column presents the methylation signals obtained from one genomic and one MSRE cel files (1-log2 of the hybridization intensities before/after MSRE treatment), as presented in our paper. Please see the README file on the Series record for associations.

source_name: Control 3 (young) MSRE2

label_protocol: As per manufacturer (Affymetrix)

extract_protocol:
Genomic DNA samples were extracted from whole peripheral blood at various israel medical centers using standard DNA extraction protocols. For DNA pooling,  DNA samples were diluted in reduced EDTA buffer (10mM Tris-HCl, 0.5mM EDTA) to a precise concentration of 50+/-0.4 ng/µl and equivalent amounts of DNA from the participating individuals were assembled in DNA pools.
One microgram of pooled genomic DNA was digested at 37oC for16 hrs with a methylation sensitive restriction enzyme (MSRE) cocktail including AciI (20 units), BsaHI (1.3 units), HhaI (2.5 units), HpaII (2.5 units), and HpyCH4IV (10 units) (NewEngland Biolabs), in a 50 microliter reaction volume with 0.1 mg/ml BSA and 10% NEB buffer #4 (New England Biolabs), ethanol precipitated, and resuspended in TE at 50 ng/µl.

value: blood

value: pool


title: Control_3_genomic_rep2

description: Hybridized to SNP 6.0

source_name: Control 3 (young) Genomic2


title: Control_3_MSRE_rep1

description: Hybridized to SNP 6.0

source_name: Control 3 (young) MSRE1


title: cl02200810.cel

tag: procedure

value: SNL


title: Control_3_genomic_rep1

description: Hybridized to SNP 6.0

source_name: Control 3 (young) Genomic1


title: NMuMG cells_MAZ1310_8hr_Biological replicate2_tech replicate 2

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
ctl5


title: Day 5 endometria from cyclic heifers normal progesterone biol rep 2

source_name: Day 5 in vivo bovine endometrium

value: cyclic


title: Day 5 endometria from cyclic heifers normal progesterone biol rep 1


title: cl02150808.cel

tag: contralateral or ipsilateral


title: Control_2_MSRE_rep2

description: Hybridized to SNP 6.0

source_name: Control 2 MSRE2


title: liver_HF_PBS_pool

source_name: liver tissue from C57Bl/6J mice fed HFD for 20 weeks, PBS injection, pool of RNA of 10 mice


title: Control_2_MSRE_rep1

description: Hybridized to SNP 6.0

source_name: Control 2 MSRE1


title: Control_2_genomic_rep2

description: Hybridized to SNP 6.0

source_name: Control 2 Genomic2


title: liver_LF_clodronate_pool

source_name: liver tissue from C57Bl/6J mice fed LFD for 20 weeks, clodronate injection, pool of RNA of 8 mice


title: NMuMG cells_MAZ1310_8hr_Biological replicate2_tech replicate 1

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
ctl4


title: Control_1_MSRE_rep1

description: Hybridized to SNP 6.0

source_name: Control 1 MSRE1


title: Control_1_MSRE_rep2

description: Hybridized to SNP 6.0

source_name: Control 1 MSRE2


title: Control_1_genomic_rep2

description: Hybridized to SNP 6.0

source_name: Control 1 Genomic2


title: cl02150816.cel

value: Sham

value: i

tag: extract


title: cl02150829.cel

tag: affy chip


title: NMuMG cells_MAZ1310_8hr_Biological replicate1_tech replicate 2

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
ctl2


title: Control_2_genomic_rep1

description: Hybridized to SNP 6.0

source_name: Control 2 Genomic1


title: cl02150817.cel


title: NMuMG cells_MAZ1310_8hr_Biological replicate1_tech replicate 3

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
ctl3


title: cl02150826.cel


title: liver_LF_PBS_pool

source_name: liver tissue from C57Bl/6J mice fed LFD for 20 weeks, PBS injection, pool of RNA of 8 mice


title: SH-SY5Y cell line with mock2 transfection (mock1 replicate)

description:
SH-SY5Y_mock2
Gene expression after mock transfection.

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing: Prior to gene expression calculations, we made a custom CDF file based on Ensembl genes. This CDF file (HGU133Plus2_Hs_ENSG.cdf) was downloaded from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.1/ensg.asp.  RMA processing was used without quantile normalization by RMA in the R Affy package (rma(normalize=F)).

source_name: SH-SY5Y neuroblastoma cell line, mock2

label_protocol: Labeling was performed according to standard Affymetrix protocols.

growth_protocol: Cells were plated in 0.5ml of growth medium, without antibiotics, 24h prior to transfection.

extract_protocol: Total RNA were extracted with Trizol reagent (Invitrogen).

treatment_protocol: miRNA mimics-Lipofectamine 2000 (Invitrogen) complexes were prepared freshly before  transfection according to the manufacturer's protocol.  SH-SY5Y and SK-N-SH cells were transfected in six-well plates using miRNA mimics-Lipofectamine 2000 with a final oligonucleotide concentration of 10nmol/L. In parallel, negative control transfections with mock oligonucleotides were conducted according to the manufacturer's protocol. For each cell line, transfections with negative control oligonucleotides were carried out in two independent replicates.

tag: cell line

value: neuroblastoma cells

tag: miRNA transfection


title: SK-N-SH cell line with mock2 transfection (mock1 replicate)

description:
SK-N-SH_mock2
Gene expression after mock transfection.

source_name: SK-N-SH neuroblastoma cell line, mock2

value: SK-N-SH


title: Control_1_genomic_rep1

description: Hybridized to SNP 6.0

source_name: Control 1 Genomic1

tag: gender


title: SH-SY5Y cell line with mock1 transfection

description:
SH-SY5Y_mock1
Gene expression after mock transfection.

source_name: SH-SY5Y neuroblastoma cell line, mock1


title: NMuMG cells_MAZ1310_8hr_Biological replicate1_tech replicate 1

description:
NMuMG cells were cultured in DMEM supplemented with 10% FBS, 10ug/ml Insulin (Sigma Aldrich) and Pen/Strep.  For treatment of NMuMG cells, cells were freshly plated into complete growth media and 45minutes later Halofuginone or MAZ1310 inactive analog diluted in acidified DMSO was added at the indicated concentrations.
ctl1

source_name: NMuMG cells, MAZ1310, 8hr


title: cl02150819.cel


title: cl02150824.cel


title: T2DM_2_MSRE_rep2

description: Hybridized to SNP 6.0

source_name: T2DM 2 MSRE2


title: cl02200805.cel


title: SK-N-SH cell line with mock1 transfection

description:
SK-N-SH_mock1
Gene expression after mock transfection.

source_name: SK-N-SH neuroblastoma cell line, mock1


title: cl02150818.cel


title: T2DM_2_MSRE_rep1

description: Hybridized to SNP 6.0

source_name: T2DM 2 MSRE1


title: SK-N-SH cell line with hsa-miR-383 transfection

description:
SK-N-SH_hsa-miR-383
Gene expression after miRNA transfection.

source_name: SK-N-SH neuroblastoma cell line, hsa-miR-383


title: cl02150825.cel