title: FIP_48hr_femaleBrain_3

description:
Ave10086_1_1rProcessedSignal
Ave10086_1_1gProcessedSignal
for gene classifier discovery

value: brain

value: FIP (fipronil) 5 ug/L for 48hr

tag: treatment

value: in water control for 48 hr


title: Early stage ovarian carcinoma T110

status: Public on Aug 22 2012

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: MAL_251901510135_S01_CGH-v4_95_Feb07_1_1.txt, MAL_251901510135_S01_CGH-v4_95_Feb07_1_2.txt

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: Dewaving: The data have been de-waved as described in Van de Wiel et al. (2009) using the R package NoWaves. This is available from www.few.vu.nl/~mavdwiel/nowaves.html. Agilent 105K normals were used as calibration. Normalization: mode normalization.

molecule: genomic DNA

organism: Homo sapiens

source_name: Tumor

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: gender

value: Female

tag: tissue

value: ovarian carcinoma tissue

tag: sample

tag: age

tag: Stage

value: Ic ascites positive

tag: type

value: E

tag: grade

tag: ct

value: no

tag: status

value: Alive

tag: os (months)

tag: progression

value: yes

tag: pfs (months)

source_name: Female reference DNA

value: blood pooled from 18 healthy individuals


title: FIP_48hr_femaleBrain_2

type: RNA

city: Cincinnati

first: Rong-Lin

last: Wang

address: 26 W MLK Dr

country: USA

institute: US EPA

description:
Ave10082_1_3rProcessedSignal
Ave10082_1_3gProcessedSignal
for gene classifier discovery

hyb_protocol: Equal amounts of Cy3- and Cy5-labeled cRNA (750 ng each) were hybridized to a zebrafish oligo microarray for 17 h at 65C. The hybridized microarrays were then washed according to the manufacturer's protocol.

scan_protocol: Scanned by a 16-bit Agilent G2565BA scanner at 10-um resolution with the red and green photomultiplier tubes set to 100% and a scan area of 61 by 21.6 mm

data_processing:
Text output of individual samples (rProcessedSignal, gProcessedSignal) from Agilent Feature Extraction software were filtered according to Agilent recommendations (feature saturation, uniformity, pixel population consistency, signal strength relative to background; Agilent Technologies Training Manual, version 4.5).  Samples were then organized either by tissue types or combined. Missing data were imputed by KNNimputer (Troyanskaya et al., 2001, Bioinformatics). This was followed by thresholding, log2 transformation, per chip normalization to 75th percentile, and per gene normation to the median of all samples [available as Series supplementary files].

The biological samples for controls were duplicated between TRI_96hr_femaleOvary and TRI_96hr_femaleOvaryLowDose as well as between TRI_96hr_maleTestis and TRI_96hr_maleTestisLowDose. These redundant controls were therefore included only once in their respective matrix files (classifier_discovery_ovary.txt, classifier_discovery_testis.txt), giving rise to their odd number of columns. In total, there are five processed/normalized matrix files either for classifier discovery or validation:

The numeric identifiers in the data matrix column headers (Sample Description field above) correspond to the unique microarray identifiers in the file names of raw text files. For example, rProcessedSignal'612' for US23502387_251322310'612'_S01_22k.txt, and Ave'10237_1_2'rProcessedSignal for US23502303_2515064'10237'_S01_GE2-v5_95_Feb07_'1_2'.txt

classifier_discovery_brain.txt: 80 treated + 80 control
classifier_discovery_ovary.txt: 105 treated + 100 control
classifier_discovery_testis.txt: 84 treated + 79 control
classifier_discovery_allTissue.txt: all three tissues combined plus 21 liver samples, 290 treated + 290 control
classifier_validation.txt: 24 treated + 28 control.

The processed/normalized data files contain rProcessedSignal and gProcessedSignal (log2 transformed, per chip and per gene normalized) from the indicated samples.

molecule: total RNA

organism: Danio rerio

source_name: brain_female_FIP_48 hr

label_protocol: Purified total RNA samples were shipped overnight on dryice to an Agilent-certified contract laboratory (Cogenics, Morrisville, NC 27560, USA), where all microarray gene expression profiling was performed. The quantity and quality of the RNA samples were assessed with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies,Wilmington, DE, USA) and an Agilent 2100 bioanalyzer. One microgram of total RNA from each sample was amplified and labeled with a fluorescent dye (either Cy3 or Cy5) with the use of a low-RNA input linear amplification labeling kit following the manufacturer's protocol). The quantity and purity of the resulting fluorescently labeled cRNA was evaluated with the Nanodrop ND-1000 spectrophotometer, and the size distribution was determined with an Agilent bioanalyzer.

growth_protocol: Reproductively mature fish were obtained from an onsite culture unit at the US EPA National Health and Human Effects Research laboratory. Three days before the initiation of exposure, fish were randomly loaded into tanks receiving a continuous flow of Lake Superior water (USA) pumped from 200 m offshore at a depth of 20 m (mesh size 1 um, flow rate 45 ml/min).  Each tank held 10 males and 10 females.

extract_protocol: Tissues were removed from RNAlater and placed on ice in 1.5-ml RNase-free microcentrifuge tubes (Ambion) containing 1 ml of TriReagent (Molecular Research Center,Cincinnati, OH)and then placed on ice for a short duration.  They were homogenized by physical disruption at 30 Hz for 5 min in a Retsch MM300 mixer mill (Retsch Laboratory Equipment, Newtown, PA, USA). Individual homogenates were immediately processed or stored at 80C in TriReagent. Total RNA was extracted following the manufacturer's protocol. Briefly, 100 ul of 1-bromo-3-chloropropane (BCP, Molecular Research Center) were added to each homogenized tissue in 1 ml of TriReagent, vortexed, and incubated at room temperature for 10 min. The BCP/TriReagent mixture was then centrifuged at 12,000 g for 15 min at 4C. The aqueous phase was transferred to a new RNase-free microcentrifuge tube containing 500 ul of 100% isopropanol and then gently agitated. Precipitated samples were centrifuged at 12,000 g for 10 min at 4C, and supernatants were decanted. One milliliter of 75% ethanol was added to the precipitant, and samples were spot vortexed and centrifuged for 10 min at 12,000 g at 4C. Supernatant was decanted, and the remaining volume was aspirated. The RNA pellets were resuspended in nuclease-free water (Ambion) by incubation at 4C for several hours. To remove any trace organic contaminants, RNA samples were reprecipitated using a 0.1 volume of 3 M sodium acetate (Ambion) and two volumes of 100% ethanol and then incubating at 80C for at least 20 min. Precipitated RNA was centrifuged at 12,000 g at 4C for 20 min, and the supernatant was removed. The RNA was resuspended in RNase-free water at 4C for several hours. The RNA was then quantified spectrophotometrically, and light absorbance at 260 and 280 nm was used as a measure of relative purity and quantity. The RNA samples were analyzed for structural integrity using either agarose gel electrophoresis or the Bioanalyzer NanoRNA kit (Agilent Technologies, Palo Alto, CA, USA). All RNA displayed 260:280-nm ratios of 1.7 or greater and had 28S:18S ratios of approximately two. Extracted total RNA was stored at 80C until subsequent use.

treatment_protocol: Reproductively mature male and female zebrafish were exposed to a continuous flow of test chemical (an analytically-confirmed concentration and a control), delivered in water (with no solvent), for 24, 48, or 96 hrs

tag: strain

value: AB

tag: genotype/variation

value: wild-type

value: 5 months

value: female

tag: treated with

source_name: brain_female_water control_48 hr


title: Early stage ovarian carcinoma T102

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: MAL_251901510132_S01_CGH-v4_95_Feb07_1_2.txt, MAL_251901510132_S01_CGH-v4_95_Feb07_1_2.txt

value: Ic capsule ruptured

value: C


title: Early stage ovarian carcinoma T103

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: MAL_251901510135_S01_CGH-v4_95_Feb07_1_2.txt, MAL_251901510135_S01_CGH-v4_95_Feb07_1_2.txt


title: mucosa-open-rep2b

city: Ashland

first: David

middle: Michael

last: Coppola

state: Virginia

address: 304 Caroline

department: Biology

institute: Randolph Macon College

hyb_protocol: Fragmented aRNA was hybridized at 42 Cº overnight using the HybBag mixing system with 1X OneArray Hybridization Buffer (Phalanx Biotech), 0.01 mg/ml sheared salmon sperm DNA (Promega, Madison, WI, USA), at a concentration of 0.025 mg/ml labeled target. After hybridization, the arrays were washed according to the standard OneArray protocol.

scan_protocol: Raw intensity signals for each microarray were captured using a Molecular Dynamics™ Axon 4100A scanner, measured using GenePixPro™ Software, and stored in GPR format (Axon Instruments, Sunnyvale, CA, USA).

data_processing:
The data from all microarrays were then analyzed using Rosetta Resolver (Rosetta Biosoftware).
Control and missing features were removed before normalization. The remaining signals were quantile normalized and transformed to log2 values.

organism: Mus musculus

source_name: olfactory mucosa

label_protocol: RNA was converted to double-stranded cDNA and amplified using in vitro transcription that included amino-allyl UTP, and the aRNA product was subsequently conjugated with with Cy5™ NHS ester (GEH Lifesciences, Piscataway, NJ, USA).

growth_protocol: Mice were kept in standard group animal room housing from birth through extraction of tissue

extract_protocol: Total RNA was extracted using Qiagen RNAeasy kit. Tissue was homogenized in 2ml dounce homogenizers and Qiashredders (Qiagen, Inc.) were used for tissue disruption. Other procedures followed the manufacturers instructions without modification.

treatment_protocol: Mice were either unilateral naris occluded with cautery or given shame cautery on mussle

value: FVB strain

value: 25 Days Old

tag: condition

value: open


title: EE2_96hr_femaleOvary_3

description:
rProcessedSignal634
gProcessedSignal634
for gene classifier discovery

source_name: ovary_female_EE2_96 hr

value: ovary

value: EE2 (17α-ethynyl estradiol) 30 ng/L for 96hr

source_name: ovary_female_water control_96 hr

tag: treatment

value: in water control for 96 hr


title: EE2_96hr_femaleOvary_2

description:
rProcessedSignal633
gProcessedSignal633
for gene classifier discovery

tag: gender


title: FIP_48hr_femaleBrain_1

description:
Ave10081_1_4rProcessedSignal
Ave10081_1_4gProcessedSignal
for gene classifier discovery

tag: tissue

value: brain

value: FIP (fipronil) 5 ug/L for 48hr

value: in water control for 48 hr


title: EE2_96hr_femaleOvary_1

description:
rProcessedSignal632
gProcessedSignal632
for gene classifier discovery


title: EE2_48hr_maleTestis_4

description:
rProcessedSignal620
gProcessedSignal620
for gene classifier discovery

source_name: testis_male_EE2_48 hr

value: male

value: testis

value: EE2 (17α-ethynyl estradiol) 30 ng/L for 48hr

source_name: testis_male_water control_48 hr


title: EE2_48hr_maleTestis_3

description:
rProcessedSignal619
gProcessedSignal619
for gene classifier discovery

value: AB

value: wild-type


title: EE2_48hr_maleTestis_2

description:
rProcessedSignal617
gProcessedSignal617
for gene classifier discovery

value: 5 months


title: FAD_96hr_femaleBrain_2

description:
rProcessedSignal654
gProcessedSignal654
for gene classifier discovery

source_name: brain_female_FAD_96 hr

value: female

value: FAD (fadrozole) 25 ug/L for 96hr

source_name: brain_female_water control_96 hr


title: mucosa-occluded-rep2b

value: FVB strain

value: Female

value: occluded


title: mucosa-occluded-rep2c

value: 25 Days Old


title: mucosa-occluded-rep2a


title: colon_PPARa-/-_heme_repl4

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: The Affymetrix GeneChip Mouse Gene 1.1 ST arrays are peg arrays arranged into the standard 96 well plate format. The 23 arrays that were used in this experiment were provided as subset of a 1x 24 array plate. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.18.1).

label: biotin

source_name: colon, PPARα knockout mouse, after 14 days on a Westernized high fat diet supplemented with heme (0.5 µmol heme/g diet), replicate 4

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Wildtype (129S1/SvImJ) and PPARα knockout (129S4/SvJae-Pparatm1Gonz/J) mice were purchased from The Jackson Laboratory and bred in our facility.

extract_protocol: Total RNA was prepared from colon using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked by 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).

treatment_protocol: Seven to nine week-old mice were placed on a Westernized high fat diet diet (40 energy% fat [mainly palm oil and corn oil] and low in calcium [30 µmol/g]), or the same diet supplemented with 0.5 µmol heme/g diet. After 14 days of intervention, mice were killed and colon was removed.

value: PPARa knockout

value: 7-9 weeks

value: colon

tag: diet

value: heme


title: colon_PPARa-/-_heme_repl5

source_name: colon, PPARα knockout mouse, after 14 days on a Westernized high fat diet supplemented with heme (0.5 µmol heme/g diet), replicate 5

tag: age


title: EE2_48hr_maleLiver_6

description:
Ave10244_1_2gProcessedSignal
Ave10244_1_2rProcessedSignal
for gene classifier discovery

source_name: liver_male_EE2_48 hr

value: liver

source_name: liver_male_water control_48 hr

value: in water control for 48 hr


title: EE2_48hr_maleBrain_5

description:
rProcessedSignal664
gProcessedSignal664
for gene classifier discovery

source_name: brain_male_EE2_48 hr

value: male

value: brain

source_name: brain_male_water control_48 hr


title: EE2_48hr_maleTestis_1

description:
rProcessedSignal616
gProcessedSignal616
for gene classifier discovery

value: AB

value: testis

value: EE2 (17α-ethynyl estradiol) 30 ng/L for 48hr


title: colon_PPARa-/-_heme_repl6

source_name: colon, PPARα knockout mouse, after 14 days on a Westernized high fat diet supplemented with heme (0.5 µmol heme/g diet), replicate 6


title: EE2_48hr_maleBrain_4

description:
rProcessedSignal615
gProcessedSignal615
for gene classifier discovery

value: wild-type

value: 5 months


title: EE2_48hr_maleLiver_5

description:
Ave10241_1_4gProcessedSignal
Ave10241_1_4rProcessedSignal
for gene classifier discovery


title: mucosa-normal-rep1a

value: FVB strain

value: normal


title: Early stage ovarian carcinoma T118

description:
reference DNA is pooled DNA from the blood of 18 healthy individuals
raw data files: MAL_251901510438_S01_CGH-v4_95_Feb07_1_1.txt, MAL_251901510438_S01_CGH-v4_95_Feb07_1_2.txt

source_name: Tumor

value: Female

value: ovarian carcinoma tissue

tag: sample

tag: Stage

value: Ic ovarian surface

value: S

value: no

value: Alive

source_name: Female reference DNA

value: blood pooled from 18 healthy individuals


title: EE2_48hr_maleBrain_3

description:
rProcessedSignal614
gProcessedSignal614
for gene classifier discovery

value: in water control for 48 hr


title: EE2_48hr_maleLiver_4

description:
Ave10240_1_3gProcessedSignal
Ave10240_1_3rProcessedSignal
for gene classifier discovery

value: male

value: liver


title: colon_PPARa-/-_heme_repl2

source_name: colon, PPARα knockout mouse, after 14 days on a Westernized high fat diet supplemented with heme (0.5 µmol heme/g diet), replicate 2

value: PPARa knockout

value: 7-9 weeks

value: colon

value: heme


title: mucosa-normal-rep1b

source_name: olfactory mucosa

value: 25 Days Old


title: EE2_48hr_maleLiver_3

description:
Ave10341_1_3rProcessedSignal
Ave10341_1_3gProcessedSignal
for gene classifier discovery

value: AB

value: wild-type

value: 5 months

value: EE2 (17α-ethynyl estradiol) 30 ng/L for 48hr


title: EE2_48hr_maleBrain_2

description:
rProcessedSignal613
gProcessedSignal613
for gene classifier discovery

value: brain


title: mucosa-open-rep2a

value: FVB strain

value: Female

value: open


title: colon_PPARa-/-_control_repl3

source_name: colon, PPARα knockout mouse, after 14 days on a Westernized high fat (control) diet, replicate 3

value: control


title: colon_PPARa-/-_control_repl6

source_name: colon, PPARα knockout mouse, after 14 days on a Westernized high fat (control) diet, replicate 6


title: colon_PPARa-/-_control_repl4

source_name: colon, PPARα knockout mouse, after 14 days on a Westernized high fat (control) diet, replicate 4


title: EE2_48hr_maleBrain_1

description:
rProcessedSignal612
gProcessedSignal612
for gene classifier discovery

value: in water control for 48 hr


title: EE2_48hr_maleLiver_2

description:
Ave10239_1_4rProcessedSignal
Ave10239_1_4gProcessedSignal
for gene classifier discovery

value: male


title: mucosa-open-rep1a


title: mucosa-normal-rep1c

value: normal


title: colon_PPARa-/-_heme_repl3

source_name: colon, PPARα knockout mouse, after 14 days on a Westernized high fat diet supplemented with heme (0.5 µmol heme/g diet), replicate 3

value: PPARa knockout


title: mucosa-open-rep1c


title: mucosa-occluded-rep1b

value: occluded


title: colon_PPARa-/-_control_repl2

source_name: colon, PPARα knockout mouse, after 14 days on a Westernized high fat (control) diet, replicate 2

value: 7-9 weeks

value: colon


title: mucosa-occluded-rep1c

value: 25 Days Old


title: mucosa-open-rep1b


title: colon_PPARa-/-_control_repl1

source_name: colon, PPARα knockout mouse, after 14 days on a Westernized high fat (control) diet, replicate 1


title: colon_WT_heme_repl5

source_name: colon, wild type mouse, after 14 days on a Westernized high fat diet supplemented with heme (0.5 µmol heme/g diet), replicate 5

value: wild type

value: heme


title: colon_WT_heme_repl6

source_name: colon, wild type mouse, after 14 days on a Westernized high fat diet supplemented with heme (0.5 µmol heme/g diet), replicate 6


title: EE2_48hr_maleLiver_1

description:
Ave10237_1_2rProcessedSignal
Ave10237_1_2gProcessedSignal
for gene classifier discovery

source_name: liver_male_EE2_48 hr

value: AB

value: wild-type

value: 5 months

value: liver


title: Anti-29a 4

city: Philadelphia

first: Joshua

last: Friedman

state: PA

address: ARC 1007B, 3615 Civic Center Blvd.

department: Pediatrics

institute: University of Pennsylvania School of Medicine

description: MiR-29a ASO 4

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Partek, using gcrma algorithm

source_name: Liver

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was purified from liver using the mirVana™ miRNA Isolation Kit (Ambion) according to the manufacturer’s instructions

treatment_protocol: Adult BALB/c female mice were injected intraperitoneally with a single dose at 20 mg per kg of antisense oligonucleotide either against miR-29a (5’-TAACCGATTTCAGATGGTGCTA-3’) or against a scrambled sequence (5’-TCATTGGCATGTACCATGCAGCT-3’ Antisense oligonucleotides contained 2’-O-methoxyethyl (2’-MOE), 2’-flouro (2’-F) 2'-alpha-flouro units with a phosphorothioate backbone (Regulus Therapeutics). Six days following the injection, liver was isolated

value: MiR-29a ASO

value: BALB/c

value: female


title: colon_PPARa-/-_heme_repl1

source_name: colon, PPARα knockout mouse, after 14 days on a Westernized high fat diet supplemented with heme (0.5 µmol heme/g diet), replicate 1


title: Anti-29a 3

description: MiR-29a ASO 3


title: array3 for wild-type MEF cells, biological (gene) rep3

city: Paris

first: Eric

last: Batsche

address: 7-9, Quai Saint Bernard

department: B2A Biological Adaptation and Ageing - UMR8256 CNRS

country: France

institute: IBPS - Institut Biologie Paris Seine

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42°C for 5 minutes centrifuge at max speed for 1 minute. • Transfer 200μl of hyb solution to each array. • Hybridize 16 hours at 45°C at 60 rpm. • Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), exon level expression were summarized from the corrected intensities and then quantile normalized.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: wild-type MEF cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the Applause WT-Amp Plus ST system Kit (NuGEN)

growth_protocol: MEF cells were grown in DMEM (Invitrogen) supplemented with 7% (v/v) fetal calf serum and 100 U.ml-1 penicillin-streptomycin

extract_protocol: Total RNA was extracted using phenol-chloroform method.  Ethanol-precipitated RNA was resuspended, treated with DNase (RNase free) 1h at 37°C, and cleaned-up using commercially available kits RNA-XS (Macherey-Nagel).

treatment_protocol: Cells were grown 3 days until subconfluency (70-80%)

tag: genotype

tag: cell type

value: embryonic fibroblast


title: colon_WT_heme_repl4

source_name: colon, wild type mouse, after 14 days on a Westernized high fat diet supplemented with heme (0.5 µmol heme/g diet), replicate 4

value: male


title: colon_WT_heme_repl1

source_name: colon, wild type mouse, after 14 days on a Westernized high fat diet supplemented with heme (0.5 µmol heme/g diet), replicate 1


title: colon_WT_heme_repl2

source_name: colon, wild type mouse, after 14 days on a Westernized high fat diet supplemented with heme (0.5 µmol heme/g diet), replicate 2


title: Anti-29a 1

description: MiR-29a ASO 1


title: mucosa-occluded-rep1a

value: FVB strain

value: Female


title: array3 for Dicer knock-out in MEF cells, biological (gene) rep3

source_name: Dicer knock-out in MEF cells

value: Dicer -/-


title: array2 for wild-type MEF cells, biological (gene) rep2


title: Control 4

description: Scramble ASO 4

value: Scramble ASO


title: Anti-29a 2

description: MiR-29a ASO 2


title: colon_WT_heme_repl3

source_name: colon, wild type mouse, after 14 days on a Westernized high fat diet supplemented with heme (0.5 µmol heme/g diet), replicate 3

value: 7-9 weeks

value: colon


title: array2 for Dicer knock-out in MEF cells, biological (gene) rep2


title: Control 2

description: Scramble ASO 2


title: array3 for Dicer knock-out in MEF cells, biological (exon) rep3


title: array1 for wild-type MEF cells, biological (gene) rep1


title: array2 for wild-type MEF cells, biological (exon) rep2


title: colon_WT_control_repl3

source_name: colon, wild type mouse, after 14 days on a Westernized high fat (control) diet, replicate 3

value: wild type

value: control


title: array1 for Dicer knock-out in MEF cells, biological (gene) rep1


title: colon_WT_control_repl5

source_name: colon, wild type mouse, after 14 days on a Westernized high fat (control) diet, replicate 5


title: Control 3

description: Scramble ASO 3


title: array3 for wild-type MEF cells, biological (exon) rep3


title: colon_WT_control_repl4

source_name: colon, wild type mouse, after 14 days on a Westernized high fat (control) diet, replicate 4


title: array1 for wild-type MEF cells, biological (exon) rep1


title: array2 for Dicer knock-out in MEF cells, biological (exon) rep2


title: array1 for Dicer knock-out in MEF cells, biological (exon) rep1


title: array3 for AGO2 knock-out in MEF cells, biological (exon) rep3

source_name: AGO2 knock-out in MEF cells


title: array3 for AGO2 knock-out in MEF cells, biological (gene) rep3


title: array2 for AGO2 knock-out in MEF cells, biological (gene) rep2


title: obacunone vs Control Replicate 1

status: Public on Aug 21 2012

city: College Station

first: Bhimanagouda

middle: S

last: Patil

state: TX

address: 1500 Research Pkwy, Ste A120

institute: Texas A&M University

hyb_protocol: A total of six slides were used. S. Typhimurium treated with obacunone cDNA was labeled with Cy3 and DMSO cDNA labeled with Cy5 were mixed and applied to three slides while the labeling was reversed for remaining three slides. This strategy was used to avoid any bias arising due to dye labeling activity of Cy3 versus Cy5. The labeled mixtures were cleaned again using QIAquick PCR purification kit (Qiagen). Equal amounts of labeled cDNA from  S. Typhimurium treatment and control were used to hybridize on the microarray slides. Hybridization was carried out at 42°C for 18 h in the dark.

scan_protocol: Scanned on a GenePix Scanner 4100A

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed test signal/processed reference signal. Acuity 4.0 (Molecular Devices) was used for analysis.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: S Typhimurium LT2_obacunone

label_protocol: Total RNA (10 µg) from treatment and control was used to synthesize cDNA using random primer for reverse transcription (Invitrogen Life Technologies, Carlsbad, CA). The primer was annealed at 70°C for 10 min, followed by snap-freezing in a dry ice-ethanol bath for 30 s and then centrifugation for 1 min. The reaction mixture (Superscript III buffer, 0.1 M dithiothreitol, and Aminoallyl-deoxyuridine triphosphate mix) was then incubated with Superscript II reverse transcriptase (Invitrogen) at 42°C overnight. Residual RNA was removed by alkaline treatment followed by neutralization, and cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified cDNAs were labeled with Cy-3 mono-Reactive Dye and Cy-5 mono-Reactive Dye (GE Health Care).

growth_protocol: Overnight culture of Salmonella Typhimurium LT2 was  diluted 1000 fold in Luria bertani broth (0.5% ) and grown to OD600 ≈ 1.0 at 37C and 200 rpm in waterbath.

extract_protocol: Total RNA was stabilized with RNAprotect bacteria reagent (Qiagen Inc., Valencia, CA, USA) and RNA was isolated with RNeasy minikit (Qiagen Inc.) according to manufacturer’s instructions.

treatment_protocol: The diluted culture was treated with 100 µg/ml (5 µl of 20 mg/ml stock) obacunone or equivalent volume of dimethyl sulfoxide (DMSO).

tag: growth stage

value: 100 µg/ml obacunone

source_name: S. Typhimurium LT2_DMSO

tag: growth satge

value: 5 µl DMSO


title: obacunone vs Control Replicate 2


title: obacunone vs Control Replicate 6


title: obacunone vs Control Replicate 4


title: obacunone vs Control Replicate 5


title: array1 for AGO2 knock-out in MEF cells, biological (gene) rep1


title: obacunone vs Control Replicate 3


title: colon_WT_control_repl1

source_name: colon, wild type mouse, after 14 days on a Westernized high fat (control) diet, replicate 1


title: Control 1

description: Scramble ASO 1


title: array1 for AGO2 knock-out in MEF cells, biological (exon) rep1


title: 0.5 μg/ml of LECT2, replicate 1

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

country: China

institute: BioChainBJ

description: Ayu macrophages from head kidney exposed to 0.5 μg/ml of LECT2 for  3.5 hours

hyb_protocol: According to the instructions of Agilent Gene Expression Hybridization Kit.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).Agilent GeneSpring GX 11.5 was used for background subtraction and LOWESS normalization.

organism: Plecoglossus altivelis

source_name: Ayu macrophages from head kidney exposed to 0 μg/ml of LECT2 for  3.5 hours

label_protocol: RNA was amplified and labeled with Cy3 using Agilent’s Low Input Quick Amp WT Labeling Kit according to the manufacturer’s instruction

growth_protocol: Macrophages were isolated from ayu head kidney. Non-adherent cells were washed off and the remaining adherent cells were incubated with RPMI 1640 medium containing 10% fetal calf serum, 50 U/mL penicillin, and 50 μg/mL streptomycin throughout the experiment.

extract_protocol: Total RNA from whole soybean sprouts about 0.5 cm long and about 5 cm long, respectively, was extracted using Trizol reagent (Invitrogen, Gaithersburg, MD) according to the manufacturer’s instructions.

treatment_protocol: Ayu macrophages were plated at 2 × 106 cells/ml in complete culture medium and incubated with 0, 0.5 or 5 μg/ml LECT2 for 3.5 hour.

tag: source tissue

value: head kidney

value: macrophage

value: 0.5 μg/ml of LECT2


title: 0 μg/ml of LECT2, replicate 2

description: Ayu macrophages from head kidney exposed to 0 μg/ml of LECT2 for  3.5 hours

value: 0 μg/ml of LECT2


title: 0 μg/ml of LECT2, replicate 1


title: 0.5 μg/ml of LECT2, replicate 2


title: WT vagina

city: Dallas

first: Ruth

middle: A

last: Word

address: 5323 Harry Hines Blvd

department: Ob-Gyn

institute: Univ TX Southwestern Med Ctr

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse 2.0 gene chips.  Chips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: WT_E2-treated vagina

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

extract_protocol: RNA isolated guanidium over cesium chloride

treatment_protocol: Ovariectomized on 11 d.  Treated with E2 (50 µg/kg/d x 3 d)

tag: strain background

value: female

value: 6 months

value: estradio (50 µg/kg/d) for 3 d

value: vagina


title: colon_WT_control_repl2

source_name: colon, wild type mouse, after 14 days on a Westernized high fat (control) diet, replicate 2

tag: strain

value: male


title: 5.0 μg/ml of LECT2, replicate 1

description: Ayu macrophages from head kidney exposed to 5.0 μg/ml of LECT2 for  3.5 hours

value: 5.0 μg/ml of LECT2


title: 5.0 μg/ml of LECT2, replicate 2


title: 0 μg/ml of LECT2, replicate 3


title: 0.5 μg/ml of LECT2, replicate 3


title: colon_PPARa-/-_control_repl5

source_name: colon, PPARα knockout mouse, after 14 days on a Westernized high fat (control) diet, replicate 5

tag: genotype/variation

value: PPARa knockout


title: 5.0 μg/ml of LECT2, replicate 3


title: Fbln5 KO vagina

source_name: Fbln5 KO_E2-treated vagina

value: Fbln5-/- (Fblin5 KO)

tag: treated with


title: STAGE Patient ID 9 FAT

city: Stockholm

first: Johan

middle: Lars Markus

last: Björkegren

state: Stockholm

address: Scheelesv. 2

department: The Department of Medical Biophysics and Biochemistry

country: Sweden

institute: The Vascular Biology Unit

description: Gene expression data from patient ID 9 visceral fat tissue during CABG

hyb_protocol: According to the standard Affymetrix protocols.

scan_protocol: The arrays scanned according to Affymetrix protocols using GeneArray Scanner 3000 and analyzed with GeneChip Operational Software 2.0.

data_processing: Gene-expression values were pre-processed with the robust multichip average (RMA) procedure in three steps (background adjustment, quantile normalization, summarization).

source_name: STAGE 9 FAT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocols.

extract_protocol: Total RNA was isolated from all biopsies with Trizol (BRL-Life Technologies) and FastPrep (MP Biomedicals) and purified with RNeasy Mini kit using DNase1 treatment (Qiagen). Sample quality was assessed with an Agilent Bioanalyzer 2100.

value: Visceral fat


title: STAGE Patient ID 66 SKLM

description: Gene expression data from patient ID 66 skeletal muscle tissue during CABG

source_name: STAGE 66 SKLM

value: Skeletal muscle


title: STAGE Patient ID 9 LIVER

description: Gene expression data from patient ID 9 liver tissue during CABG

source_name: STAGE 9 LIVER

value: Liver


title: STAGE Patient ID 66 FAT

description: Gene expression data from patient ID 66 visceral fat tissue during CABG

source_name: STAGE 66 FAT


title: STAGE Patient ID 66 MAMMARY

description: Gene expression data from patient ID 66 internal mammary artery tissue during CABG

source_name: STAGE 66 MAMMARY

value: Internal mammary artery


title: STAGE Patient ID 8 LIVER

description: Gene expression data from patient ID 8 liver tissue during CABG

source_name: STAGE 8 LIVER


title: STAGE Patient ID 66 LIVER

description: Gene expression data from patient ID 66 liver tissue during CABG

source_name: STAGE 66 LIVER


title: STAGE Patient ID 66 STANS

description: Gene expression data from patient ID 66 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 66 STANS

value: Atherosclerotic aortic wall


title: STAGE Patient ID 7 SKLM

description: Gene expression data from patient ID 7 skeletal muscle tissue during CABG

source_name: STAGE 7 SKLM


title: STAGE Patient ID 8 SKLM

description: Gene expression data from patient ID 8 skeletal muscle tissue during CABG

source_name: STAGE 8 SKLM


title: STAGE Patient ID 65 STANS

description: Gene expression data from patient ID 65 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 65 STANS


title: STAGE Patient ID 65 SKLM

description: Gene expression data from patient ID 65 skeletal muscle tissue during CABG

source_name: STAGE 65 SKLM


title: STAGE Patient ID 65 LIVER

description: Gene expression data from patient ID 65 liver tissue during CABG

source_name: STAGE 65 LIVER


title: STAGE Patient ID 64 SKLM

description: Gene expression data from patient ID 64 skeletal muscle tissue during CABG

source_name: STAGE 64 SKLM


title: STAGE Patient ID 7 LIVER

description: Gene expression data from patient ID 7 liver tissue during CABG

source_name: STAGE 7 LIVER


title: STAGE Patient ID 64 MAMMARY

description: Gene expression data from patient ID 64 internal mammary artery tissue during CABG

source_name: STAGE 64 MAMMARY


title: STAGE Patient ID 65 MAMMARY

description: Gene expression data from patient ID 65 internal mammary artery tissue during CABG

source_name: STAGE 65 MAMMARY


title: STAGE Patient ID 8 FAT

description: Gene expression data from patient ID 8 visceral fat tissue during CABG

source_name: STAGE 8 FAT


title: STAGE Patient ID 64 STANS

description: Gene expression data from patient ID 64 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 64 STANS


title: STAGE Patient ID 7 FAT

description: Gene expression data from patient ID 7 visceral fat tissue during CABG

source_name: STAGE 7 FAT


title: STAGE Patient ID 9 SKLM

description: Gene expression data from patient ID 9 skeletal muscle tissue during CABG

source_name: STAGE 9 SKLM


title: STAGE Patient ID 63 LIVER

description: Gene expression data from patient ID 63 liver tissue during CABG

source_name: STAGE 63 LIVER


title: STAGE Patient ID 64 LIVER

description: Gene expression data from patient ID 64 liver tissue during CABG

source_name: STAGE 64 LIVER


title: STAGE Patient ID 63 SKLM

description: Gene expression data from patient ID 63 skeletal muscle tissue during CABG

source_name: STAGE 63 SKLM


title: STAGE Patient ID 65 FAT

description: Gene expression data from patient ID 65 visceral fat tissue during CABG

source_name: STAGE 65 FAT


title: STAGE Patient ID 63 FAT

description: Gene expression data from patient ID 63 visceral fat tissue during CABG

source_name: STAGE 63 FAT


title: STAGE Patient ID 61 STANS

description: Gene expression data from patient ID 61 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 61 STANS


title: STAGE Patient ID 62 SKLM

description: Gene expression data from patient ID 62 skeletal muscle tissue during CABG

source_name: STAGE 62 SKLM


title: STAGE Patient ID 62 FAT

description: Gene expression data from patient ID 62 visceral fat tissue during CABG

source_name: STAGE 62 FAT


title: STAGE Patient ID 64 FAT

description: Gene expression data from patient ID 64 visceral fat tissue during CABG

source_name: STAGE 64 FAT


title: STAGE Patient ID 62 LIVER

description: Gene expression data from patient ID 62 liver tissue during CABG

source_name: STAGE 62 LIVER


title: STAGE Patient ID 61 FAT

description: Gene expression data from patient ID 61 visceral fat tissue during CABG

source_name: STAGE 61 FAT


title: STAGE Patient ID 60 STANS

description: Gene expression data from patient ID 60 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 60 STANS


title: STAGE Patient ID 60 MAMMARY

description: Gene expression data from patient ID 60 internal mammary artery tissue during CABG

source_name: STAGE 60 MAMMARY


title: STAGE Patient ID 61 LIVER

description: Gene expression data from patient ID 61 liver tissue during CABG

source_name: STAGE 61 LIVER


title: STAGE Patient ID 61 MAMMARY

description: Gene expression data from patient ID 61 internal mammary artery tissue during CABG

source_name: STAGE 61 MAMMARY


title: STAGE Patient ID 61 SKLM

description: Gene expression data from patient ID 61 skeletal muscle tissue during CABG

source_name: STAGE 61 SKLM


title: STAGE Patient ID 59 MAMMARY

description: Gene expression data from patient ID 59 internal mammary artery tissue during CABG

source_name: STAGE 59 MAMMARY


title: STAGE Patient ID 58 LIVER

description: Gene expression data from patient ID 58 liver tissue during CABG

source_name: STAGE 58 LIVER


title: STAGE Patient ID 60 FAT

description: Gene expression data from patient ID 60 visceral fat tissue during CABG

source_name: STAGE 60 FAT


title: STAGE Patient ID 60 SKLM

description: Gene expression data from patient ID 60 skeletal muscle tissue during CABG

source_name: STAGE 60 SKLM


title: STAGE Patient ID 6 FAT

description: Gene expression data from patient ID 6 visceral fat tissue during CABG

source_name: STAGE 6 FAT


title: STAGE Patient ID 59 STANS

description: Gene expression data from patient ID 59 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 59 STANS


title: STAGE Patient ID 59 SKLM

description: Gene expression data from patient ID 59 skeletal muscle tissue during CABG

source_name: STAGE 59 SKLM


title: STAGE Patient ID 6 SKLM

description: Gene expression data from patient ID 6 skeletal muscle tissue during CABG

source_name: STAGE 6 SKLM


title: STAGE Patient ID 59 FAT

description: Gene expression data from patient ID 59 visceral fat tissue during CABG

source_name: STAGE 59 FAT


title: STAGE Patient ID 58 SKLM

description: Gene expression data from patient ID 58 skeletal muscle tissue during CABG

source_name: STAGE 58 SKLM


title: STAGE Patient ID 60 LIVER

description: Gene expression data from patient ID 60 liver tissue during CABG

source_name: STAGE 60 LIVER


title: STAGE Patient ID 58 MAMMARY

description: Gene expression data from patient ID 58 internal mammary artery tissue during CABG

source_name: STAGE 58 MAMMARY


title: STAGE Patient ID 57 SKLM

description: Gene expression data from patient ID 57 skeletal muscle tissue during CABG

source_name: STAGE 57 SKLM


title: STAGE Patient ID 6 LIVER

description: Gene expression data from patient ID 6 liver tissue during CABG

source_name: STAGE 6 LIVER


title: STAGE Patient ID 58 STANS

description: Gene expression data from patient ID 58 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 58 STANS


title: STAGE Patient ID 59 LIVER

description: Gene expression data from patient ID 59 liver tissue during CABG

source_name: STAGE 59 LIVER


title: STAGE Patient ID 55 STANS

description: Gene expression data from patient ID 55 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 55 STANS


title: STAGE Patient ID 57 LIVER

description: Gene expression data from patient ID 57 liver tissue during CABG

source_name: STAGE 57 LIVER


title: STAGE Patient ID 54 STANS

description: Gene expression data from patient ID 54 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 54 STANS


title: STAGE Patient ID 55 LIVER

description: Gene expression data from patient ID 55 liver tissue during CABG

source_name: STAGE 55 LIVER


title: STAGE Patient ID 56 SKLM

description: Gene expression data from patient ID 56 skeletal muscle tissue during CABG

source_name: STAGE 56 SKLM


title: STAGE Patient ID 55 SKLM

description: Gene expression data from patient ID 55 skeletal muscle tissue during CABG

source_name: STAGE 55 SKLM


title: STAGE Patient ID 58 FAT

description: Gene expression data from patient ID 58 visceral fat tissue during CABG

source_name: STAGE 58 FAT


title: STAGE Patient ID 56 FAT

description: Gene expression data from patient ID 56 visceral fat tissue during CABG

source_name: STAGE 56 FAT


title: array2 for AGO2 knock-out in MEF cells, biological (exon) rep2

source_name: AGO2 knock-out in MEF cells

value: embryonic fibroblast


title: STAGE Patient ID 56 LIVER

description: Gene expression data from patient ID 56 liver tissue during CABG

source_name: STAGE 56 LIVER


title: STAGE Patient ID 55 FAT

description: Gene expression data from patient ID 55 visceral fat tissue during CABG

source_name: STAGE 55 FAT


title: STAGE Patient ID 54 FAT

description: Gene expression data from patient ID 54 visceral fat tissue during CABG

source_name: STAGE 54 FAT


title: STAGE Patient ID 54 LIVER

description: Gene expression data from patient ID 54 liver tissue during CABG

source_name: STAGE 54 LIVER


title: STAGE Patient ID 53 MAMMARY

description: Gene expression data from patient ID 53 internal mammary artery tissue during CABG

source_name: STAGE 53 MAMMARY


title: STAGE Patient ID 53 STANS

description: Gene expression data from patient ID 53 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 53 STANS


title: STAGE Patient ID 52 FAT

description: Gene expression data from patient ID 52 visceral fat tissue during CABG

source_name: STAGE 52 FAT


title: STAGE Patient ID 53 LIVER

description: Gene expression data from patient ID 53 liver tissue during CABG

source_name: STAGE 53 LIVER


title: STAGE Patient ID 52 SKLM

description: Gene expression data from patient ID 52 skeletal muscle tissue during CABG

source_name: STAGE 52 SKLM


title: STAGE Patient ID 53 FAT

description: Gene expression data from patient ID 53 visceral fat tissue during CABG

source_name: STAGE 53 FAT


title: STAGE Patient ID 52 MAMMARY

description: Gene expression data from patient ID 52 internal mammary artery tissue during CABG

source_name: STAGE 52 MAMMARY


title: STAGE Patient ID 52 LIVER

description: Gene expression data from patient ID 52 liver tissue during CABG

source_name: STAGE 52 LIVER


title: STAGE Patient ID 51 SKLM

description: Gene expression data from patient ID 51 skeletal muscle tissue during CABG

source_name: STAGE 51 SKLM


title: STAGE Patient ID 52 STANS

description: Gene expression data from patient ID 52 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 52 STANS


title: STAGE Patient ID 51 FAT

description: Gene expression data from patient ID 51 visceral fat tissue during CABG

source_name: STAGE 51 FAT


title: STAGE Patient ID 51 STANS

description: Gene expression data from patient ID 51 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 51 STANS


title: STAGE Patient ID 51 MAMMARY

description: Gene expression data from patient ID 51 internal mammary artery tissue during CABG

source_name: STAGE 51 MAMMARY


title: STAGE Patient ID 51 LIVER

description: Gene expression data from patient ID 51 liver tissue during CABG

source_name: STAGE 51 LIVER


title: STAGE Patient ID 5 SKLM

description: Gene expression data from patient ID 5 skeletal muscle tissue during CABG

source_name: STAGE 5 SKLM


title: STAGE Patient ID 50 LIVER

description: Gene expression data from patient ID 50 liver tissue during CABG

source_name: STAGE 50 LIVER


title: STAGE Patient ID 50 STANS

description: Gene expression data from patient ID 50 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 50 STANS


title: STAGE Patient ID 49 SKLM

description: Gene expression data from patient ID 49 skeletal muscle tissue during CABG

source_name: STAGE 49 SKLM


title: STAGE Patient ID 5 LIVER

description: Gene expression data from patient ID 5 liver tissue during CABG

source_name: STAGE 5 LIVER


title: STAGE Patient ID 50 FAT

description: Gene expression data from patient ID 50 visceral fat tissue during CABG

source_name: STAGE 50 FAT


title: STAGE Patient ID 50 SKLM

description: Gene expression data from patient ID 50 skeletal muscle tissue during CABG

source_name: STAGE 50 SKLM


title: STAGE Patient ID 5 FAT

description: Gene expression data from patient ID 5 visceral fat tissue during CABG

source_name: STAGE 5 FAT


title: STAGE Patient ID 47 SKLM

description: Gene expression data from patient ID 47 skeletal muscle tissue during CABG

source_name: STAGE 47 SKLM


title: STAGE Patient ID 49 LIVER

description: Gene expression data from patient ID 49 liver tissue during CABG

source_name: STAGE 49 LIVER


title: STAGE Patient ID 47 FAT

description: Gene expression data from patient ID 47 visceral fat tissue during CABG

source_name: STAGE 47 FAT


title: STAGE Patient ID 49 FAT

description: Gene expression data from patient ID 49 visceral fat tissue during CABG

source_name: STAGE 49 FAT


title: STAGE Patient ID 48 FAT

description: Gene expression data from patient ID 48 visceral fat tissue during CABG

source_name: STAGE 48 FAT


title: STAGE Patient ID 47 LIVER

description: Gene expression data from patient ID 47 liver tissue during CABG

source_name: STAGE 47 LIVER


title: STAGE Patient ID 46 MAMMARY

description: Gene expression data from patient ID 46 internal mammary artery tissue during CABG

source_name: STAGE 46 MAMMARY


title: STAGE Patient ID 46 STANS

description: Gene expression data from patient ID 46 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 46 STANS


title: STAGE Patient ID 47 STANS

description: Gene expression data from patient ID 47 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 47 STANS


title: STAGE Patient ID 48 MAMMARY

description: Gene expression data from patient ID 48 internal mammary artery tissue during CABG

source_name: STAGE 48 MAMMARY


title: STAGE Patient ID 47 MAMMARY

description: Gene expression data from patient ID 47 internal mammary artery tissue during CABG

source_name: STAGE 47 MAMMARY


title: STAGE Patient ID 50 MAMMARY

description: Gene expression data from patient ID 50 internal mammary artery tissue during CABG

source_name: STAGE 50 MAMMARY


title: STAGE Patient ID 55 MAMMARY

description: Gene expression data from patient ID 55 internal mammary artery tissue during CABG

source_name: STAGE 55 MAMMARY


title: STAGE Patient ID 46 SKLM

description: Gene expression data from patient ID 46 skeletal muscle tissue during CABG

source_name: STAGE 46 SKLM


title: STAGE Patient ID 57 FAT

description: Gene expression data from patient ID 57 visceral fat tissue during CABG

source_name: STAGE 57 FAT


title: STAGE Patient ID 48 STANS

description: Gene expression data from patient ID 48 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 48 STANS


title: STAGE Patient ID 48 SKLM

description: Gene expression data from patient ID 48 skeletal muscle tissue during CABG

source_name: STAGE 48 SKLM


title: STAGE Patient ID 46 LIVER

description: Gene expression data from patient ID 46 liver tissue during CABG

source_name: STAGE 46 LIVER


title: STAGE Patient ID 46 FAT

description: Gene expression data from patient ID 46 visceral fat tissue during CABG

source_name: STAGE 46 FAT


title: STAGE Patient ID 48 LIVER

description: Gene expression data from patient ID 48 liver tissue during CABG

source_name: STAGE 48 LIVER


title: STAGE Patient ID 45 SKLM

description: Gene expression data from patient ID 45 skeletal muscle tissue during CABG

source_name: STAGE 45 SKLM


title: STAGE Patient ID 45 LIVER

description: Gene expression data from patient ID 45 liver tissue during CABG

source_name: STAGE 45 LIVER


title: STAGE Patient ID 45 FAT

description: Gene expression data from patient ID 45 visceral fat tissue during CABG

source_name: STAGE 45 FAT


title: STAGE Patient ID 45 MAMMARY

description: Gene expression data from patient ID 45 internal mammary artery tissue during CABG

source_name: STAGE 45 MAMMARY


title: STAGE Patient ID 45 STANS

description: Gene expression data from patient ID 45 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 45 STANS


title: STAGE Patient ID 44 SKLM

description: Gene expression data from patient ID 44 skeletal muscle tissue during CABG

source_name: STAGE 44 SKLM


title: STAGE Patient ID 44 STANS

description: Gene expression data from patient ID 44 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 44 STANS


title: STAGE Patient ID 44 LIVER

description: Gene expression data from patient ID 44 liver tissue during CABG

source_name: STAGE 44 LIVER


title: STAGE Patient ID 44 FAT

description: Gene expression data from patient ID 44 visceral fat tissue during CABG

source_name: STAGE 44 FAT


title: STAGE Patient ID 44 MAMMARY

description: Gene expression data from patient ID 44 internal mammary artery tissue during CABG

source_name: STAGE 44 MAMMARY


title: STAGE Patient ID 43 SKLM

description: Gene expression data from patient ID 43 skeletal muscle tissue during CABG

source_name: STAGE 43 SKLM


title: STAGE Patient ID 43 FAT

description: Gene expression data from patient ID 43 visceral fat tissue during CABG

source_name: STAGE 43 FAT


title: STAGE Patient ID 42 SKLM

description: Gene expression data from patient ID 42 skeletal muscle tissue during CABG

source_name: STAGE 42 SKLM


title: STAGE Patient ID 43 LIVER

description: Gene expression data from patient ID 43 liver tissue during CABG

source_name: STAGE 43 LIVER


title: STAGE Patient ID 42 LIVER

description: Gene expression data from patient ID 42 liver tissue during CABG

source_name: STAGE 42 LIVER


title: STAGE Patient ID 4 SKLM

description: Gene expression data from patient ID 4 skeletal muscle tissue during CABG

source_name: STAGE 4 SKLM


title: STAGE Patient ID 39 SKLM

description: Gene expression data from patient ID 39 skeletal muscle tissue during CABG

source_name: STAGE 39 SKLM


title: STAGE Patient ID 42 FAT

description: Gene expression data from patient ID 42 visceral fat tissue during CABG

source_name: STAGE 42 FAT


title: STAGE Patient ID 42 MAMMARY

description: Gene expression data from patient ID 42 internal mammary artery tissue during CABG

source_name: STAGE 42 MAMMARY


title: STAGE Patient ID 40 FAT

description: Gene expression data from patient ID 40 visceral fat tissue during CABG

source_name: STAGE 40 FAT


title: STAGE Patient ID 41 STANS

description: Gene expression data from patient ID 41 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 41 STANS


title: STAGE Patient ID 40 SKLM

description: Gene expression data from patient ID 40 skeletal muscle tissue during CABG

source_name: STAGE 40 SKLM


title: STAGE Patient ID 41 SKLM

description: Gene expression data from patient ID 41 skeletal muscle tissue during CABG

source_name: STAGE 41 SKLM


title: STAGE Patient ID 41 FAT

description: Gene expression data from patient ID 41 visceral fat tissue during CABG

source_name: STAGE 41 FAT


title: STAGE Patient ID 4 FAT

description: Gene expression data from patient ID 4 visceral fat tissue during CABG

source_name: STAGE 4 FAT


title: STAGE Patient ID 4 LIVER

description: Gene expression data from patient ID 4 liver tissue during CABG

source_name: STAGE 4 LIVER


title: STAGE Patient ID 39 LIVER

description: Gene expression data from patient ID 39 liver tissue during CABG

source_name: STAGE 39 LIVER


title: STAGE Patient ID 41 MAMMARY

description: Gene expression data from patient ID 41 internal mammary artery tissue during CABG

source_name: STAGE 41 MAMMARY


title: STAGE Patient ID 39 MAMMARY

description: Gene expression data from patient ID 39 internal mammary artery tissue during CABG

source_name: STAGE 39 MAMMARY


title: STAGE Patient ID 40 LIVER

description: Gene expression data from patient ID 40 liver tissue during CABG

source_name: STAGE 40 LIVER


title: STAGE Patient ID 39 FAT

description: Gene expression data from patient ID 39 visceral fat tissue during CABG

source_name: STAGE 39 FAT


title: STAGE Patient ID 39 STANS

description: Gene expression data from patient ID 39 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 39 STANS


title: STAGE Patient ID 53 SKLM

description: Gene expression data from patient ID 53 skeletal muscle tissue during CABG

source_name: STAGE 53 SKLM


title: STAGE Patient ID 42 STANS

description: Gene expression data from patient ID 42 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 42 STANS


title: STAGE Patient ID 41 LIVER

description: Gene expression data from patient ID 41 liver tissue during CABG

source_name: STAGE 41 LIVER


title: STAGE Patient ID 54 MAMMARY

description: Gene expression data from patient ID 54 internal mammary artery tissue during CABG

source_name: STAGE 54 MAMMARY


title: STAGE Patient ID 37 SKLM

description: Gene expression data from patient ID 37 skeletal muscle tissue during CABG

source_name: STAGE 37 SKLM


title: STAGE Patient ID 38 LIVER

description: Gene expression data from patient ID 38 liver tissue during CABG

source_name: STAGE 38 LIVER


title: STAGE Patient ID 54 SKLM

description: Gene expression data from patient ID 54 skeletal muscle tissue during CABG

source_name: STAGE 54 SKLM


title: STAGE Patient ID 38 FAT

description: Gene expression data from patient ID 38 visceral fat tissue during CABG

source_name: STAGE 38 FAT


title: STAGE Patient ID 37 STANS

description: Gene expression data from patient ID 37 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 37 STANS


title: STAGE Patient ID 37 FAT

description: Gene expression data from patient ID 37 visceral fat tissue during CABG

source_name: STAGE 37 FAT


title: STAGE Patient ID 36 MAMMARY

description: Gene expression data from patient ID 36 internal mammary artery tissue during CABG

source_name: STAGE 36 MAMMARY


title: STAGE Patient ID 37 MAMMARY

description: Gene expression data from patient ID 37 internal mammary artery tissue during CABG

source_name: STAGE 37 MAMMARY


title: STAGE Patient ID 36 STANS

description: Gene expression data from patient ID 36 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 36 STANS


title: STAGE Patient ID 37 LIVER

description: Gene expression data from patient ID 37 liver tissue during CABG

source_name: STAGE 37 LIVER


title: STAGE Patient ID 36 LIVER

description: Gene expression data from patient ID 36 liver tissue during CABG

source_name: STAGE 36 LIVER


title: STAGE Patient ID 33 LIVER

description: Gene expression data from patient ID 33 liver tissue during CABG

source_name: STAGE 33 LIVER


title: STAGE Patient ID 35 FAT

description: Gene expression data from patient ID 35 visceral fat tissue during CABG

source_name: STAGE 35 FAT


title: STAGE Patient ID 34 FAT

description: Gene expression data from patient ID 34 visceral fat tissue during CABG

source_name: STAGE 34 FAT


title: STAGE Patient ID 36 SKLM

description: Gene expression data from patient ID 36 skeletal muscle tissue during CABG

source_name: STAGE 36 SKLM


title: STAGE Patient ID 34 SKLM

description: Gene expression data from patient ID 34 skeletal muscle tissue during CABG

source_name: STAGE 34 SKLM


title: STAGE Patient ID 35 SKLM

description: Gene expression data from patient ID 35 skeletal muscle tissue during CABG

source_name: STAGE 35 SKLM


title: STAGE Patient ID 34 LIVER

description: Gene expression data from patient ID 34 liver tissue during CABG

source_name: STAGE 34 LIVER


title: STAGE Patient ID 35 MAMMARY

description: Gene expression data from patient ID 35 internal mammary artery tissue during CABG

source_name: STAGE 35 MAMMARY


title: STAGE Patient ID 35 STANS

description: Gene expression data from patient ID 35 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 35 STANS


title: STAGE Patient ID 33 SKLM

description: Gene expression data from patient ID 33 skeletal muscle tissue during CABG

source_name: STAGE 33 SKLM


title: STAGE Patient ID 35 LIVER

description: Gene expression data from patient ID 35 liver tissue during CABG

source_name: STAGE 35 LIVER


title: STAGE Patient ID 32 SKLM

description: Gene expression data from patient ID 32 skeletal muscle tissue during CABG

source_name: STAGE 32 SKLM


title: STAGE Patient ID 32 LIVER

description: Gene expression data from patient ID 32 liver tissue during CABG

source_name: STAGE 32 LIVER


title: STAGE Patient ID 31 SKLM

description: Gene expression data from patient ID 31 skeletal muscle tissue during CABG

source_name: STAGE 31 SKLM


title: STAGE Patient ID 33 FAT

description: Gene expression data from patient ID 33 visceral fat tissue during CABG

source_name: STAGE 33 FAT


title: STAGE Patient ID 32 FAT

description: Gene expression data from patient ID 32 visceral fat tissue during CABG

source_name: STAGE 32 FAT


title: STAGE Patient ID 36 FAT

description: Gene expression data from patient ID 36 visceral fat tissue during CABG

source_name: STAGE 36 FAT


title: STAGE Patient ID 30 FAT

description: Gene expression data from patient ID 30 visceral fat tissue during CABG

source_name: STAGE 30 FAT


title: STAGE Patient ID 31 LIVER

description: Gene expression data from patient ID 31 liver tissue during CABG

source_name: STAGE 31 LIVER


title: STAGE Patient ID 31 FAT

description: Gene expression data from patient ID 31 visceral fat tissue during CABG

source_name: STAGE 31 FAT


title: STAGE Patient ID 3 FAT

description: Gene expression data from patient ID 3 visceral fat tissue during CABG

source_name: STAGE 3 FAT


title: STAGE Patient ID 30 SKLM

description: Gene expression data from patient ID 30 skeletal muscle tissue during CABG

source_name: STAGE 30 SKLM


title: STAGE Patient ID 30 LIVER

description: Gene expression data from patient ID 30 liver tissue during CABG

source_name: STAGE 30 LIVER


title: STAGE Patient ID 29 SKLM

description: Gene expression data from patient ID 29 skeletal muscle tissue during CABG

source_name: STAGE 29 SKLM


title: STAGE Patient ID 29 MAMMARY

description: Gene expression data from patient ID 29 internal mammary artery tissue during CABG

source_name: STAGE 29 MAMMARY


title: STAGE Patient ID 29 STANS

description: Gene expression data from patient ID 29 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 29 STANS


title: STAGE Patient ID 3 LIVER

description: Gene expression data from patient ID 3 liver tissue during CABG

source_name: STAGE 3 LIVER


title: STAGE Patient ID 28 LIVER

description: Gene expression data from patient ID 28 liver tissue during CABG

source_name: STAGE 28 LIVER


title: STAGE Patient ID 3 SKLM

description: Gene expression data from patient ID 3 skeletal muscle tissue during CABG

source_name: STAGE 3 SKLM


title: STAGE Patient ID 28 SKLM

description: Gene expression data from patient ID 28 skeletal muscle tissue during CABG

source_name: STAGE 28 SKLM


title: STAGE Patient ID 29 LIVER

description: Gene expression data from patient ID 29 liver tissue during CABG

source_name: STAGE 29 LIVER


title: STAGE Patient ID 27 LIVER

description: Gene expression data from patient ID 27 liver tissue during CABG

source_name: STAGE 27 LIVER


title: STAGE Patient ID 27 SKLM

description: Gene expression data from patient ID 27 skeletal muscle tissue during CABG

source_name: STAGE 27 SKLM


title: STAGE Patient ID 27 MAMMARY

description: Gene expression data from patient ID 27 internal mammary artery tissue during CABG

source_name: STAGE 27 MAMMARY


title: STAGE Patient ID 28 STANS

description: Gene expression data from patient ID 28 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 28 STANS


title: STAGE Patient ID 27 STANS

description: Gene expression data from patient ID 27 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 27 STANS


title: STAGE Patient ID 28 MAMMARY

description: Gene expression data from patient ID 28 internal mammary artery tissue during CABG

source_name: STAGE 28 MAMMARY


title: STAGE Patient ID 28 FAT

description: Gene expression data from patient ID 28 visceral fat tissue during CABG

source_name: STAGE 28 FAT


title: STAGE Patient ID 29 FAT

description: Gene expression data from patient ID 29 visceral fat tissue during CABG

source_name: STAGE 29 FAT


title: STAGE Patient ID 26 SKLM

description: Gene expression data from patient ID 26 skeletal muscle tissue during CABG

source_name: STAGE 26 SKLM


title: STAGE Patient ID 26 STANS

description: Gene expression data from patient ID 26 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 26 STANS


title: STAGE Patient ID 26 MAMMARY

description: Gene expression data from patient ID 26 internal mammary artery tissue during CABG

source_name: STAGE 26 MAMMARY


title: STAGE Patient ID 27 FAT

description: Gene expression data from patient ID 27 visceral fat tissue during CABG

source_name: STAGE 27 FAT


title: STAGE Patient ID 25 STANS

description: Gene expression data from patient ID 25 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 25 STANS


title: STAGE Patient ID 26 LIVER

description: Gene expression data from patient ID 26 liver tissue during CABG

source_name: STAGE 26 LIVER


title: STAGE Patient ID 38 SKLM

description: Gene expression data from patient ID 38 skeletal muscle tissue during CABG

source_name: STAGE 38 SKLM


title: STAGE Patient ID 26 FAT

description: Gene expression data from patient ID 26 visceral fat tissue during CABG

source_name: STAGE 26 FAT


title: STAGE Patient ID 25 LIVER

description: Gene expression data from patient ID 25 liver tissue during CABG

source_name: STAGE 25 LIVER


title: STAGE Patient ID 25 SKLM

description: Gene expression data from patient ID 25 skeletal muscle tissue during CABG

source_name: STAGE 25 SKLM


title: STAGE Patient ID 25 MAMMARY

description: Gene expression data from patient ID 25 internal mammary artery tissue during CABG

source_name: STAGE 25 MAMMARY


title: STAGE Patient ID 24 MAMMARY

description: Gene expression data from patient ID 24 internal mammary artery tissue during CABG

source_name: STAGE 24 MAMMARY


title: STAGE Patient ID 25 FAT

description: Gene expression data from patient ID 25 visceral fat tissue during CABG

source_name: STAGE 25 FAT


title: STAGE Patient ID 24 FAT

description: Gene expression data from patient ID 24 visceral fat tissue during CABG

source_name: STAGE 24 FAT


title: STAGE Patient ID 24 SKLM

description: Gene expression data from patient ID 24 skeletal muscle tissue during CABG

source_name: STAGE 24 SKLM


title: STAGE Patient ID 24 LIVER

description: Gene expression data from patient ID 24 liver tissue during CABG

source_name: STAGE 24 LIVER


title: STAGE Patient ID 24 STANS

description: Gene expression data from patient ID 24 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 24 STANS


title: STAGE Patient ID 23 SKLM

description: Gene expression data from patient ID 23 skeletal muscle tissue during CABG

source_name: STAGE 23 SKLM


title: STAGE Patient ID 23 STANS

description: Gene expression data from patient ID 23 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 23 STANS


title: STAGE Patient ID 23 MAMMARY

description: Gene expression data from patient ID 23 internal mammary artery tissue during CABG

source_name: STAGE 23 MAMMARY


title: STAGE Patient ID 23 FAT

description: Gene expression data from patient ID 23 visceral fat tissue during CABG

source_name: STAGE 23 FAT


title: STAGE Patient ID 22 STANS

description: Gene expression data from patient ID 22 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 22 STANS


title: STAGE Patient ID 22 SKLM

description: Gene expression data from patient ID 22 skeletal muscle tissue during CABG

source_name: STAGE 22 SKLM


title: STAGE Patient ID 23 LIVER

description: Gene expression data from patient ID 23 liver tissue during CABG

source_name: STAGE 23 LIVER


title: STAGE Patient ID 22 MAMMARY

description: Gene expression data from patient ID 22 internal mammary artery tissue during CABG

source_name: STAGE 22 MAMMARY


title: STAGE Patient ID 22 LIVER

description: Gene expression data from patient ID 22 liver tissue during CABG

source_name: STAGE 22 LIVER


title: STAGE Patient ID 22 FAT

description: Gene expression data from patient ID 22 visceral fat tissue during CABG

source_name: STAGE 22 FAT


title: STAGE Patient ID 21 STANS

description: Gene expression data from patient ID 21 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 21 STANS


title: Elk_27271102

city: Uppsala

first: Matthew

last: Webster

address: Box 582

department: IMBIM

institute: Uppsala University

hyb_protocol: Standard NimbleGen protocols (http://www.nimblegen.com/products/lit/05434483001.pdf)

organism: Canis lupus familiaris

source_name: [test] EDTA blood from pedigreed Swedish Elkhound

extract_protocol: Genomic DNA was purified using commercial purification kits and the quality of the DNA was analyzed by spectrophotometry and agarose gel electrophoresis.

tag: breed

value: Swedish Elkhound

source_name: [reference] EDTA blood from pedigreed Boxer

value: Boxer

value: Male


title: STAGE Patient ID 21 SKLM

description: Gene expression data from patient ID 21 skeletal muscle tissue during CABG

source_name: STAGE 21 SKLM


title: Wlf_27212102

scan_protocol: Standard NimbleGen protocols (http://www.nimblegen.com/products/lit/05434483001.pdf)

organism: Canis lupus

source_name: [test] EDTA blood from pedigreed Wolf


title: Wlf_27744002

data_processing: Standard NimbleGen protocols (http://www.nimblegen.com/products/lit/05434483001.pdf)


title: Wlf_27736802

label_protocol: Standard NimbleGen protocols (http://www.nimblegen.com/products/lit/05434483001.pdf)

value: female


title: Sch_27370102

source_name: [test] EDTA blood from pedigreed Schnauzer

value: Schnauzer


title: LRe_27206202

source_name: [test] EDTA blood from pedigreed Labrador Retriever

value: Labrador Retriever


title: Sch_27222802


title: STAGE Patient ID 21 MAMMARY

description: Gene expression data from patient ID 21 internal mammary artery tissue during CABG

source_name: STAGE 21 MAMMARY


title: STAGE Patient ID 21 FAT

description: Gene expression data from patient ID 21 visceral fat tissue during CABG

source_name: STAGE 21 FAT


title: Elk_27875902


title: STAGE Patient ID 21 LIVER

description: Gene expression data from patient ID 21 liver tissue during CABG

source_name: STAGE 21 LIVER


title: NSD_27239202

source_name: [test] EDTA blood from pedigreed Nova Scotia Duck Tolling Retriever

value: Nova Scotia Duck Tolling Retriever


title: STAGE Patient ID 20 SKLM

description: Gene expression data from patient ID 20 skeletal muscle tissue during CABG

source_name: STAGE 20 SKLM


title: NSD_27244502


title: LRe_27205802

value: male


title: STAGE Patient ID 20 MAMMARY

description: Gene expression data from patient ID 20 internal mammary artery tissue during CABG

source_name: STAGE 20 MAMMARY


title: STAGE Patient ID 20 STANS

description: Gene expression data from patient ID 20 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 20 STANS


title: STAGE Patient ID 20 LIVER

description: Gene expression data from patient ID 20 liver tissue during CABG

source_name: STAGE 20 LIVER


title: IrW_27263902

source_name: [test] EDTA blood from pedigreed Irish Wolfhound

value: Irish Wolfhound


title: Pdl_27735602

source_name: [test] EDTA blood from pedigreed Poodle

value: Poodle


title: Pdl_27224302


title: Sar_27214602

source_name: [test] EDTA blood from pedigreed Sarloos

value: Sarloos


title: STAGE Patient ID 20 FAT

description: Gene expression data from patient ID 20 visceral fat tissue during CABG

source_name: STAGE 20 FAT

value: Visceral fat


title: IrW_27231002

source_name: [reference] EDTA blood from pedigreed Boxer


title: Sar_27206502


title: IrW_27245102


title: IrW_27232202


title: IrW_27238902


title: GRe_27743102

source_name: [test] EDTA blood from pedigreed Golden Retriever

value: Golden Retriever


title: STAGE Patient ID 19 STANS

description: Gene expression data from patient ID 19 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 19 STANS


title: IrW_27244202


title: STAGE Patient ID 2 FAT

description: Gene expression data from patient ID 2 visceral fat tissue during CABG

source_name: STAGE 2 FAT


title: STAGE Patient ID 2 SKLM

description: Gene expression data from patient ID 2 skeletal muscle tissue during CABG

source_name: STAGE 2 SKLM

value: Skeletal muscle


title: IrW_27230702


title: IrW_27237702


title: STAGE Patient ID 2 LIVER

description: Gene expression data from patient ID 2 liver tissue during CABG

source_name: STAGE 2 LIVER

value: Liver


title: STAGE Patient ID 19 SKLM

description: Gene expression data from patient ID 19 skeletal muscle tissue during CABG

source_name: STAGE 19 SKLM


title: IrW_27366602


title: STAGE Patient ID 19 MAMMARY

description: Gene expression data from patient ID 19 internal mammary artery tissue during CABG

source_name: STAGE 19 MAMMARY

value: Internal mammary artery


title: GRe_27737102


title: STAGE Patient ID 19 FAT

description: Gene expression data from patient ID 19 visceral fat tissue during CABG

source_name: STAGE 19 FAT


title: GRe_27735902


title: STAGE Patient ID 19 LIVER

description: Gene expression data from patient ID 19 liver tissue during CABG

source_name: STAGE 19 LIVER


title: GRe_27219402


title: STAGE Patient ID 18 STANS

description: Gene expression data from patient ID 18 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 18 STANS

value: Atherosclerotic aortic wall


title: GRe_27216102


title: STAGE Patient ID 18 MAMMARY

description: Gene expression data from patient ID 18 internal mammary artery tissue during CABG

source_name: STAGE 18 MAMMARY


title: GRe_28059802


title: STAGE Patient ID 18 SKLM

description: Gene expression data from patient ID 18 skeletal muscle tissue during CABG

source_name: STAGE 18 SKLM


title: STAGE Patient ID 18 LIVER

description: Gene expression data from patient ID 18 liver tissue during CABG

source_name: STAGE 18 LIVER


title: STAGE Patient ID 18 FAT

description: Gene expression data from patient ID 18 visceral fat tissue during CABG

source_name: STAGE 18 FAT


title: STAGE Patient ID 17 STANS

description: Gene expression data from patient ID 17 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 17 STANS


title: STAGE Patient ID 17 SKLM

description: Gene expression data from patient ID 17 skeletal muscle tissue during CABG

source_name: STAGE 17 SKLM


title: STAGE Patient ID 17 MAMMARY

description: Gene expression data from patient ID 17 internal mammary artery tissue during CABG

source_name: STAGE 17 MAMMARY


title: GRe_27213602

source_name: [test] EDTA blood from pedigreed Golden Retriever

source_name: [reference] EDTA blood from pedigreed Boxer


title: STAGE Patient ID 16 SKLM

description: Gene expression data from patient ID 16 skeletal muscle tissue during CABG

source_name: STAGE 16 SKLM


title: STAGE Patient ID 16 MAMMARY

description: Gene expression data from patient ID 16 internal mammary artery tissue during CABG

source_name: STAGE 16 MAMMARY


title: STAGE Patient ID 17 LIVER

description: Gene expression data from patient ID 17 liver tissue during CABG

source_name: STAGE 17 LIVER


title: GRe_27213302


title: STAGE Patient ID 16 LIVER

description: Gene expression data from patient ID 16 liver tissue during CABG

source_name: STAGE 16 LIVER


title: STAGE Patient ID 16 STANS

description: Gene expression data from patient ID 16 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 16 STANS


title: STAGE Patient ID 16 FAT

description: Gene expression data from patient ID 16 visceral fat tissue during CABG

source_name: STAGE 16 FAT


title: STAGE Patient ID 17 FAT

description: Gene expression data from patient ID 17 visceral fat tissue during CABG

source_name: STAGE 17 FAT


title: STAGE Patient ID 15 STANS

description: Gene expression data from patient ID 15 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 15 STANS


title: STAGE Patient ID 15 SKLM

description: Gene expression data from patient ID 15 skeletal muscle tissue during CABG

source_name: STAGE 15 SKLM


title: STAGE Patient ID 15 LIVER

description: Gene expression data from patient ID 15 liver tissue during CABG

source_name: STAGE 15 LIVER


title: STAGE Patient ID 15 MAMMARY

description: Gene expression data from patient ID 15 internal mammary artery tissue during CABG

source_name: STAGE 15 MAMMARY


title: GRe_27209002


title: GRe_27213002


title: STAGE Patient ID 14 STANS

description: Gene expression data from patient ID 14 atherosclerotic aortic wall tissue during CABG

source_name: STAGE 14 STANS


title: STAGE Patient ID 14 SKLM

description: Gene expression data from patient ID 14 skeletal muscle tissue during CABG

source_name: STAGE 14 SKLM


title: STAGE Patient ID 13 SKLM

description: Gene expression data from patient ID 13 skeletal muscle tissue during CABG

source_name: STAGE 13 SKLM


title: STAGE Patient ID 15 FAT

description: Gene expression data from patient ID 15 visceral fat tissue during CABG

source_name: STAGE 15 FAT


title: STAGE Patient ID 12 SKLM

description: Gene expression data from patient ID 12 skeletal muscle tissue during CABG

source_name: STAGE 12 SKLM


title: STAGE Patient ID 14 MAMMARY

description: Gene expression data from patient ID 14 internal mammary artery tissue during CABG

source_name: STAGE 14 MAMMARY


title: STAGE Patient ID 13 FAT

description: Gene expression data from patient ID 13 visceral fat tissue during CABG

source_name: STAGE 13 FAT


title: STAGE Patient ID 14 FAT

description: Gene expression data from patient ID 14 visceral fat tissue during CABG

source_name: STAGE 14 FAT


title: FSp_27747502

source_name: [test] EDTA blood from pedigreed Finnish Spitz

value: Finnish Spitz

source_name: [reference] EDTA blood from pedigreed Boxer


title: STAGE Patient ID 14 LIVER

description: Gene expression data from patient ID 14 liver tissue during CABG

source_name: STAGE 14 LIVER


title: STAGE Patient ID 13 LIVER

description: Gene expression data from patient ID 13 liver tissue during CABG

source_name: STAGE 13 LIVER


title: STAGE Patient ID 12 LIVER

description: Gene expression data from patient ID 12 liver tissue during CABG

source_name: STAGE 12 LIVER


title: ESS_27231902

source_name: [test] EDTA blood from pedigreed English Springer Spaniel

value: English Springer Spaniel

value: Boxer


title: STAGE Patient ID 11 SKLM

description: Gene expression data from patient ID 11 skeletal muscle tissue during CABG

source_name: STAGE 11 SKLM


title: STAGE Patient ID 11 LIVER

description: Gene expression data from patient ID 11 liver tissue during CABG

source_name: STAGE 11 LIVER


title: S.pyogenes_5448AP_rep3

city: St Lucia

first: Peter

middle: G

last: Maamary

address: Cooper Road

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: University of Queensland

description: RNA extracted from mid-log bacteria in vitro by mechanical disruption and the Qiagen Rneasy Kit. RNA converted to Cy-labelled cDNA using the Agilent FairPlay III Microarray Labeling Kit. cDNA hybridized to JCVI PFGRC Streptococcus pyogenes v2 oligo arrays.

hyb_protocol: Hybridization to JCVI PFGRC Streptococcus pyogenes v2 arrays were performed precisely as outlined by the array manufacturer.

scan_protocol: Slides were scanned using the GenePix 4000B scanner (Axon Instruments, Inc.)

data_processing: As arrays were performed using a single color method with Cy3, only data collected in this channel was used for analysis. Probes representing M1 core genes (MGAS5005 and SF370) were selected for analysis. All ORFs within prophage sequences and the 36 kb slo and nga encoding SNP-rich region were excluded for analysis. After filtering the probe set, background subtracted median fluorescence values for each probe were compiled into a single file for upload into GeneSpring GX 11.5 (Agilent), threshold set to 20 fluorescence units and percentile shift to 75% with no baseline correction.

organism: Streptococcus pyogenes

source_name: isolate5448AP_mid-log_in vitro

label_protocol: RNA was converted to cDNA and coupled with Cy3 monoreactive dye using the Agilent Fairplay III Microarray labelling kit.

growth_protocol: Cultures in Todd-Hewitt with 1% yeast extract were initiated with 0.1 volume overnight growth and grown to mid-log phase

extract_protocol: At mid-log growth, cultures were treated with 0.1 M Tris-Cl (pH 6.8), 2mM EDTA, 0.06% Azide and bacteria collected by centrifugation. Cells were lysed by mechanical disruption and RNA purified using the Qiagen RNeasy mini kit. Contaminating DNA was removed with the Qiagen RNase-free DNase Set

tag: growth phase and conditions

value: mid-logarithmic phase in vitro

tag: covrs status

value: mutant

tag: sdad2 genotype

value: positive

tag: spea2 genotype


title: IrW_27257502

source_name: [test] EDTA blood from pedigreed Irish Wolfhound

tag: gender

value: Male


title: STAGE Patient ID 10 FAT

description: Gene expression data from patient ID 10 visceral fat tissue during CABG

source_name: STAGE 10 FAT

tag: tissue


title: Chi_27253802

source_name: [test] EDTA blood from pedigreed Chihuahua

value: Chihuahua

value: male


title: STAGE Patient ID 10 LIVER

description: Gene expression data from patient ID 10 liver tissue during CABG

source_name: STAGE 10 LIVER


title: ECS_27765702

source_name: [test] EDTA blood from pedigreed English Cocker Spaniel

value: English Cocker Spaniel


title: STAGE Patient ID 10 SKLM

description: Gene expression data from patient ID 10 skeletal muscle tissue during CABG

source_name: STAGE 10 SKLM


title: STAGE Patient ID 11 FAT

description: Gene expression data from patient ID 11 visceral fat tissue during CABG

source_name: STAGE 11 FAT


title: GSh_27359802

source_name: [test] EDTA blood from pedigreed German Shepherd

value: German Shepherd

value: female


title: ECS_27289802


title: S.pyogenes_5448_rep3

source_name: isolate5448_mid-log_in vitro

value: intact


title: FSp_27221202

source_name: [test] EDTA blood from pedigreed Finnish Spitz

source_name: [reference] EDTA blood from pedigreed Boxer


title: GSh_27238002


title: S.pyogenes_GT94052_rep3

source_name: isolateGT94052_mid-log_in vitro


title: STAGE Patient ID 1 LIVER

description: Gene expression data from patient ID 1 liver tissue during CABG

source_name: STAGE 1 LIVER


title: Box_27220602

source_name: [test] EDTA blood from pedigreed Boxer


title: S.pyogenes_GT94966_rep3

source_name: isolateGT94966_mid-log_in vitro


title: ESS_27290202_01

source_name: [test] EDTA blood from pedigreed English Springer Spaniel


title: Chi_27376902


title: CCS_27220302

source_name: [test] EDTA blood from pedigreed Cavalier King Charles Spaniel

value: Cavalier King Charles Spaniel


title: STAGE Patient ID 12 FAT

description: Gene expression data from patient ID 12 visceral fat tissue during CABG

source_name: STAGE 12 FAT

value: Visceral fat


title: S.pyogenes_90223_rep3

source_name: isolate90223_mid-log_in vitro


title: GFP3

city: New York

first: Omar

last: Abdel-Wahab

state: NY

address: 1275 York Ave.

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

description: GFP control

hyb_protocol: Please see AffymetrixExpression Analysis Technical Manual (http://www.affymetrix.com/estore/browse/products.jsp?categoryIdClicked=&productId=131415#1_3)

data_processing: RMA : log2 transform : Quantile Normalization : Median Polish using Partek Genomics Suite Version 6.5

source_name: Normal CD34+ Cord Blood

label_protocol: Please refer to Affymetrix 3' IVT Express Kit Documentaion (http://www.affymetrix.com/estore/browse/products.jsp?categoryIdClicked=&productId=131415#1_3)

growth_protocol: CD34+ cells were cultured in serum-free stem cell expansion media (StemSPAN SFEM; StemCell Technologies) supplemented with SCF (100 ng/mL), IL-3 (20 ng/mL), and IL-6 (10 ng/mL), every other day.

extract_protocol: RNA was extracted using TRIZOL according to manufacturers guidelines

treatment_protocol: CD34+ cells were transfected with shRNA for ASXL1 or vector control after 24 hours in culture using the 4D-Nucleofector system according to the manufacturer's protocol from Lonza (Walkersville, MD)

tag: treatment

value: GFP


title: GFP2

description: GFP control

scan_protocol: Please see AffymetrixExpression Analysis Technical Manual (http://www.affymetrix.com/estore/browse/products.jsp?categoryIdClicked=&productId=131415#1_3)


title: S.pyogenes_AB3574_rep3

source_name: isolateAB3574_mid-log_in vitro


title: S.pyogenes_SF370_rep3

source_name: isolateSF370_mid-log_in vitro

value: negative


title: S.pyogenes_NS696_rep3

source_name: isolateNS696_mid-log_in vitro


title: GFP1

description: GFP control


title: Dac_27222502

source_name: [test] EDTA blood from pedigreed Dachshund

value: Dachshund


title: S.pyogenes_5448AP_rep2

source_name: isolate5448AP_mid-log_in vitro


title: S.pyogenes_L485_rep3

source_name: isolateL485_mid-log_in vitro


title: S.pyogenes_5448_rep2

source_name: isolate5448_mid-log_in vitro


title: S.pyogenes_GT94966_rep2


title: S.pyogenes_5636_rep2

source_name: isolate5636_mid-log_in vitro


title: ASXL1siRNA3

description: ASXL1 short hairpin


title: Dac_27327102

source_name: [reference] EDTA blood from pedigreed Boxer


title: S.pyogenes_GT94052_rep2

source_name: isolateGT94052_mid-log_in vitro


title: S.pyogenes_AB3574_rep2


title: STAGE Patient ID 1 SKLM

description: Gene expression data from patient ID 1 skeletal muscle tissue during CABG

source_name: STAGE 1 SKLM

value: Skeletal muscle


title: S.pyogenes_89158_rep3

source_name: isolate89158_mid-log_in vitro


title: S.pyogenes_NS696_rep2


title: Tumor tissue of esophagus with family history

city: Hong Kong

first: Grace

last: Fu

address: 21 Sassoon Road

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

description:
EC-FH_2
Gene expression data from tumor tissues of ESCC patients with family history

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix Human Genome U133 Plus 2.0 GeneChip. GeneChips were washed and stained.

source_name: tumor tissue RNA from ESCC patient with family history

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

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

value: esophageal tissue


title: S.pyogenes_AB1551_rep2

source_name: isolateAB1551_mid-log_in vitro

value: mid-logarithmic phase in vitro


title: BTe_27227402

source_name: [test] EDTA blood from pedigreed Border Terrier

value: Border Terrier

value: Boxer


title: STAGE Patient ID 1 FAT

description: Gene expression data from patient ID 1 visceral fat tissue during CABG

source_name: STAGE 1 FAT


title: Box_27220902

source_name: [test] EDTA blood from pedigreed Boxer

value: Male


title: ASXL1siRNA1

description: ASXL1 short hairpin

source_name: Normal CD34+ Cord Blood


title: S.pyogenes_L485_rep2


title: S.pyogenes_89158_rep2


title: S.pyogenes_5448AP_rep1

value: mutant

value: positive


title: S.pyogenes_5448_rep1


title: S.pyogenes_5636_rep3


title: S.pyogenes_SF370_rep2

source_name: isolateSF370_mid-log_in vitro


title: S.pyogenes_5636_rep1


title: BTe_27800302

value: male


title: S.pyogenes_GT94966_rep1

source_name: isolateGT94966_mid-log_in vitro


title: S.pyogenes_GT94052_rep1


title: S.pyogenes_AB3574_rep1

source_name: isolateAB3574_mid-log_in vitro


title: S.pyogenes_90223_rep1

source_name: isolate90223_mid-log_in vitro


title: S.pyogenes_AB1551_rep1


title: S.pyogenes_SF370_rep1


title: S.pyogenes_NS696_rep1

source_name: isolateNS696_mid-log_in vitro


title: S.pyogenes_AB1551_rep3


title: Vector-2

description: GFP control

source_name: UKE1 cell line

growth_protocol: UKE1 cells were grown in RPMI-1640 medium supplemented with 10% FBS + 1mM hydrocortisone + 10% horse serum

treatment_protocol: UKE1 cells were transduced with lentivirus containing shRNA for ASXL1 or vector control in a pLKO.1-puromycin vector followed by puromycin selection for at least 2 weeks


title: Vector-4

description: GFP control


title: AI4 from AI4 mice, biological replicate 2

city: Bronx

first: Juan

last: Lin

address: 1300 Morris Park Ave.

institute: Albert Einstein College of Medicine

description:
Gene expression data
Sample name: XZ.PAN.U.8712

hyb_protocol: Samples were hybridized according to the standard Affymetrix protocol

scan_protocol: Gene ST 1.0 chips were scanned using Affymetrix 7G

data_processing:
Data were analyzed using Affymetrix GenChip operating software 1.4 and the quality tested using the Affymetrix Expression Console.
All positive, negative and spike-in control probe sets and probe sets without mRNA Description information were not included in the analysis.

source_name: AI4 from AI4 mice

label_protocol: Samples were labeled according to the standard Affymetrix protocol

growth_protocol: Single-cell suspensions of pancreata  from AI4 mice or Rip-B7xAI4 mice were pooled and AI4αβ CD8 T cells were isolated by FACS sorting using anti-CD8 Ab and MimA2/H-2Db tetramer

extract_protocol: Total RNA was purified according to manufacturrer's instructions using Qiagen Rnesway kit

value: C57BL/6.H2g7/g7 background

tag: disease status

value: developed T1D

value: pancreas

value: AI4αβ CD8 T cells


title: Vector-1

description: GFP control


title: S.pyogenes_L485_rep1

source_name: isolateL485_mid-log_in vitro

value: intact


title: AI4 from Rip-B7xAI4 mice, biological replicate 3

description:
Gene expression data
Sample name: XZ.PAN.T.8718

source_name: AI4 from Rip-B7xAI4 mice

value: resistant to T1D

tag: cell type


title: grapefruit peel, rep3

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

description: control, replicate 3

hyb_protocol: according to the instruction manual, as described in the Affymetrix website

data_processing: RMA normalization, summarization by mean, done by Partek Genomics suite (version 6.5 Copyright © 2010)

organism: Citrus x paradisi

source_name: grapefruit peel

extract_protocol: SV Total RNA Isolation System (Promega, Madison, WI, USA)

value: fruit peel


title: AI4 from Rip-B7xAI4 mice, biological replicate 1

description:
Gene expression data
Sample name: XZ.PAN.T.9249


title: grapefruit peel, Metschnikowia fructicola treatment, rep2

description: Metschnikowia fructicola (mf) treatment, rep2

scan_protocol: according to the instruction manual, as described in the Affymetrix website


title: AI4 from AI4 mice, biological replicate 3

description:
Gene expression data
Sample name: XZ.PAN.U.8717


title: grapefruit peel, Metschnikowia fructicola treatment, rep3

description: Metschnikowia fructicola (mf) treatment, rep3

label_protocol: according to the instruction manual, as described in the Affymetrix website


title: Vector-3

description: GFP control

value: GFP


title: Wild-type Type II 9_27_04

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing: Data was processed/normalized by MAS 5.0 using Affymetrix Expression Console version 1.1.

source_name: SPC WT lung adult

extract_protocol: standard Affymetrix protocol

tag: sample type

value: Primary culture of type II cells collected from SPC WT lung (adult)

tag: age

value: adult

value: type II lung epithelial

tag: genotype

value: Surfactant Proteiin C WT

tag: genetic background


title: S.pyogenes_89158_rep1

source_name: isolate89158_mid-log_in vitro

tag: strain

value: mid-logarithmic phase in vitro

value: negative


title: Wild-type Type II 1_8_9_04

source_name: SPC WT lung (adult)

value: Primary culture of typeII cells collected from SPC WT lung (adult)


title: AI4 from Rip-B7xAI4 mice, biological replicate 2

description:
Gene expression data
Sample name: XZ.PAN.T.8715

tag: genotype/variation


title: KO SPC Type II 2_8_9_04

source_name: SPC KO lung adult

value: Primary culture of typeII cells collected from SPC KO lung adult

value: Surfactant Proteiin C KO


title: ASXL_Hrpn2-3

description: ASXL1 short hairpin


title: grapefruit peel, Metschnikowia fructicola treatment, rep1

description: Metschnikowia fructicola (mf) treatment, rep1


title: AI4 from AI4 mice, biological replicate 1

description:
Gene expression data
Sample name: XZ.PAN.U.9248

value: C57BL/6.H2g7/g7 background


title: 252800512010-1

status: Public on Aug 20 2012

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: F WT SHAM #3

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: OneChannelGui analysis, interslide quantile normalization.

source_name: F WT SHAM #3

label_protocol:
Agilent - Low RNA input QuickAmp
amp protocol:  cRNA Agilent

extract_protocol: Qiagen

value: Adrenal gland

tag: amount in (µg)

value: Female

value: Sham

value: WT

tag: rin number


title: grapefruit peel, rep2

description: control, replicate 2


title: ASXL_Hrpn2-2-2

description: ASXL1 short hairpin


title: 252800512010-2

description: F WT TESTO #3

source_name: F WT TESTO #3

value: Testosterone


title: ASXL_Hrpn2-1

description: ASXL1 short hairpin


title: ASXL_Hrpn2-2

description: ASXL1 short hairpin


title: 252800510950-2

description: M WT CAST #3

source_name: M WT CAST #3

value: Adrenal Gland

value: Male

value: Castration


title: 252800510950-4

description: M T1 KO CAST #3

source_name: M T1 KO CAST #3


title: 252800510950-8

description: F T1 KO TESTO #3

source_name: F T1 KO TESTO #3


title: 252800510949-8

description: F T1 KO TESTO #2

source_name: F T1 KO TESTO #2


title: grapefruit peel, rep 1

description: control, replicate 1

value: fruit peel


title: 252800510949-6

description: F WT TESTO #2

source_name: F WT TESTO #2


title: KO SPC Type II 9_27_04

value: Primary culture of type II cells collected from SPC KO lung adult

value: adult

value: type II lung epithelial


title: 252800510950-3

description: M T1 KO SHAM #3

source_name: M T1 KO SHAM #3


title: 252800510950-7

description: F T1 KO SHAM #3

source_name: F T1 KO SHAM #3


title: 252800510949-5

description: F WT SHAM #2

source_name: F WT SHAM #2


title: 252800510950-1

description: M WT SHAM #3

source_name: M WT SHAM #3


title: 252800510949-7

description: F T1 KO SHAM #2

source_name: F T1 KO SHAM #2


title: 252800510949-4

description: M T1 KO CAST #2

source_name: M T1 KO CAST #2


title: CCS_27221502

source_name: [test] EDTA blood from pedigreed Cavalier King Charles Spaniel

tag: breed

value: Cavalier King Charles Spaniel

value: female

source_name: [reference] EDTA blood from pedigreed Boxer

value: Boxer


title: 252800510948-8

description: F T1 KO TESTO #1

source_name: F T1 KO TESTO #1


title: 252800510949-1

description: M WT SHAM #2

source_name: M WT SHAM #2


title: 252800510948-7

description: F T1 KO SHAM #1

source_name: F T1 KO SHAM #1


title: 252800510948-4

description: M T1 KO CAST #1

source_name: M T1 KO CAST #1


title: 252800510949-2

description: M WT CAST #2

source_name: M WT CAST #2


title: 252800510948-5

description: F WT SHAM #1

source_name: F WT SHAM #1


title: 252800510949-3

description: M T1 KO SHAM #2

source_name: M T1 KO SHAM #2


title: 252800510948-3

description: M T1 KO SHAM #1

source_name: M T1 KO SHAM #1


title: 252800510948-2

description: M WT CAST #1

source_name: M WT CAST #1


title: 252800510948-6

description: F WT TESTO #1

source_name: F WT TESTO #1


title: Rb_E2F1_carcinoma_rep5

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

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

data_processing: The data were analyzed with RMA using RMAExpress.

source_name: skin carcinoma, tamoxifen tretaed

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

extract_protocol: Extraction of total RNA was performed with RNeasy Qiagen Kit according to the manufacturer's instructions.

treatment_protocol: Tamoxifen treatment was topicallyadministered in the shaved backskin of animals (2x2 cm) at 20 mg/per day dissolved in DMSO/acetone for 5 consecutive days.

value: FVB/N


title: 252800510948-1

description: M WT SHAM #1

source_name: M WT SHAM #1


title: Rb_E2F1_carcinoma_rep6


title: Rb_E2F1_carcinoma_rep7


title: Rb_E2F1_carcinoma_rep8


title: Rb_E2F1_carcinoma_rep4


title: Rb_E2F1_carcinoma_rep3


title: Rb_E2F1_skin_rep2

source_name: skin tissue, tamoxifen tretaed


title: Rb_E2F1_carcinoma_rep1


title: Normal_skin_rep5

value: Normal


title: E2F1_skin_rep1


title: Normal_skin_rep4


title: Rb_E2F1_carcinoma_rep2


title: E2F1_skin_rep3


title: Rb_E2F1_skin_rep1


title: Rb_skin_rep2

value: Rb


title: S.pyogenes_90223_rep2

description: RNA extracted from mid-log bacteria in vitro by mechanical disruption and the Qiagen Rneasy Kit. RNA converted to Cy-labelled cDNA using the Agilent FairPlay III Microarray Labeling Kit. cDNA hybridized to JCVI PFGRC Streptococcus pyogenes v2 oligo arrays.

source_name: isolate90223_mid-log_in vitro

tag: growth phase and conditions

value: mid-logarithmic phase in vitro

tag: covrs status

value: intact

value: positive


title: Rb_skin_rep1


title: Normal_skin_rep3


title: rectum_8wk_gnoto_2

city: Madison

last: Geiger

state: WI

address: 1400 University Ave

department: Surgery

institute: UW-Madison

description: stripping protocol:Stripping protocol came from the following reference: Journal of Biotechnology 128 (2007) 1-13

hyb_protocol: Agilent Two-Color Microarray-Based Gene Expression Analysis 17hrs 65 deg celcius Surehyb chamber

scan_protocol: Agilent Technologies Scanner G2505B US22502567 5um 16bit

data_processing: Agilent Feature extraction versions 9.1 and 9..5 for background subtraction - Local background subtraction and normalization Linear LOWESS.

source_name: Gnoto rectum 3.4

label_protocol: Total RNA was amplified and labeled according to manufactures instructions. Agilent Two-Color Microarray-Based Gene Expression Analysis Agilent low RNA input linear amplification kit, PLUS

growth_protocol: Ad lib feeding and drinking.  12hours light:12hours dark. ZT0=time lights turn on the room ~6:00 AM.

extract_protocol: Polytron 10 seconds  and processed with an Qiagen Rneasy Mini kit

treatment_protocol: Mice are sacrificed and large intestines removed, rinsed well and mucosa scraped or whole organ was used.  Mucosa or whole organ is homogenized with a polytron.

tag: stripped array

value: Yes

value: 8 weeks

tag: number of pooled samples

value: rectum muc

value: wild type

source_name: SIRC

value: 10 weeks

value: Small intestine, colon, rectum


title: colon_8wk_gnoto_3

source_name: Gnoto colon 3

tag: tissue

value: colon muc


title: rectum_8wk_gnoto_4

value: No

source_name: Gnoto rectum 8,11


title: rectum_4wk_3

source_name: 4wk rectum 4,5

value: 4 weeks

value: rectum


title: colon_8wk_gnoto_5

source_name: Gnoto colon 8,11


title: rectum_8wk_gnoto_1

source_name: Gnoto rectum 1.2


title: rectum_8wk_gnoto_3

source_name: Gnoto rectum 3


title: rectum_4wk_2

source_name: 4wk rectum 2,3


title: rectum_4wk_1

source_name: 4wk rectum 1


title: colon_4wk_2

source_name: 4wk colon 2,3

value: colon


title: Normal_skin_rep1

value: FVB/N


title: colon_8wk_gnoto_4

source_name: Gnoto colon 3 (replicate)


title: rectum_1wk_3

source_name: 1wk rectum 4,5

value: 1 week


title: Normal_skin_rep2

value: Normal


title: colon_8wk_gnoto_1

source_name: Gnoto colon 1.2


title: colon_8wk_gnoto_2

source_name: Gnoto colon 3.4


title: colon_4wk_1

source_name: 4wk colon 1


title: colon_4wk_3

source_name: 4wk colon 4,5