title: MH4

description: Gene expression in heart left atrium of adult male mouse

source_name: Male_hetrozygous_Replicate 4

growth_protocol: Heterozygous Brd2+/- females were mated to heterozygous Brd2+/- males. Male mice of the 7th generation of backcrossing onto a C57Bl/6J background strain were used so that their genetic background could be considered on average 99% C57Bl/6J (Mouse Nomenclature, jaxmice.jax.org). Mice genotypes were assessed by PCR using primers that spanned the gene-trap vector junction inserted into the Brd2 gene.

treatment_protocol: Frontal cortex was removed and the striatum disected and snap frozen.

value: Male


title: MSC-0 rep 3

status: Public on Sep 01 2015

type: RNA

city: Houston

first: Xiaoping

last: Sun

state: Texas

address: 2130 Westholcombe Blvd, LSP12.3014

department: Laboratory Medicine

country: USA

institute: The University of Texas MD Anderson Cancer Center

hyb_protocol: Standard Illumina hybridization protocol was used.

scan_protocol: Standard Illumina scanning protocol was used.

data_processing: Background correction and quantile normalization was performed by R/Bioconductor package limma (Linear Models for Microarray Data, version 3.14.4).

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: OP9 MSCs

label_protocol: Biotinylated cRNA was prepared as per standard protocol provided in Illumina TotalPrep RNA Amplification Kit .

extract_protocol: RNA was isolated from vehicle or imatinib treated MSCs with the TRI Reagent (Ambion). During RNA precipitation, 20 µg of linear polyacrylamide (Ambion) was added to isopropanol (Sigma), and precipitated RNA was gently washed once with n-butanol (Sigma) and twice with 70% alcohol before air-dried RNA pellets were dissolved in diethylpyrocarbonate-treated water (Fisher Scientific).

tag: strain

value: B6C3F1 op/op

tag: agent

value: vehicle

tag: time point (hrs)

tag: tissue

value: Newborn Calvaria

tag: cell type

value: MSCs


title: MSC-0 rep 2


title: FW1

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Gene expression in striatum of adult female mouse

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

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

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction vs.11 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.

source_name: Female_wildtype_Replicate 1

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

growth_protocol: Heterozygous Brd2+/- females were mated to heterozygous Brd2+/- males. Mice of the 7th generation of backcrossing onto a C57Bl/6J background strain were used so that their genetic background could be considered on average 99% C57Bl/6J (Mouse Nomenclature, jaxmice.jax.org). Mice genotypes were assessed by PCR using primers that spanned the gene-trap vector junction inserted into the Brd2 gene.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a Thermo Scientific NanoDrop ND-2000 and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: The striatum was disected and snap frozen.

tag: Sex

value: Female

value: Prefrontal cortex striatum

tag: develomental stage

value: adult


title: MSC-0 rep 1


title: 24-N,Normal thyroid,N0

city: Anderlecht

first: Maxime

last: Tarabichi

state: Bruxelles

address: Route de Lennik 808

country: Belgium

institute: IRIBHM

hyb_protocol: Genome wide mRNA profiles were obtained through hybridization of samples onto Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays.

scan_protocol: according to standard Affymetrix protocols

data_processing: Data analyses were performed in R v.3.1.0. The arrays used contain 54 613 probe sets representing 20 027 genes.CEL files, which contain the raw data, were normalized using the fRMA normalization method from the fRMA package v.1.6.0 (hgu133plus2frmavecs v.1.1.8) with default parameters.To annotate the probe sets, R packages annotate v1.32.3 and hgu133plus2.db v2.6.3 were used.

label: biotin

organism: Homo sapiens

source_name: 24-N,Normal thyroid,N0

extract_protocol: RNA extraction was performed using RNeasy Mini Kit columns (Qiagen, Hilden, Germany).

treatment_protocol: The samples used in this study were derived from 31 patients diagnosed for PTC and were chosen based on sample availability and RNA quality rather than clinical parameters. Thereby the samples consist of a variety of classical PTC and PTC variants with various pathological characteristics. Samples were obtained from the Jules Bordet Institute (Brussels, Belgium), and La Pitié-Salpêtrière Hospital (Paris, France).

tag: rqi

value: F

tag: tnm

tag: Stage

value: I

value: Trabecular

value: left

tag: multifocal

value: no

value: BRAFmut


title: 22a-PT-N0,Papillary thyroid carcinoma,N0

label_protocol: according to standard Affymetrix protocols

value: M

value: III

value: Papillary

value: right

value: yes


title: MH1

source_name: Male_hetrozygous_Replicate 1

value: Male


title: MH2

source_name: Male_hetrozygous_Replicate 2


title: MH3

source_name: Male_hetrozygous_Replicate 3


title: 17-PT-N1,Papillary thyroid carcinoma,N1

source_name: 17-PT-N1,Papillary thyroid carcinoma,N1

value: both

value: 1 on 6


title: 9-PT-N1,Papillary thyroid carcinoma,N1

source_name: 9-PT-N1,Papillary thyroid carcinoma,N1


title: Leaf_ISP_23C_rep3

city: East Lansing

first: Thomas

middle: D

last: Sharkey

state: MI

address: 603 Wilson Rd

department: Biochemistry and Molecular Biology

institute: Michigan State University

description: Gene expression after 24 hours in 20 ppm isoprene at 23 °C

hyb_protocol: Labeled RNA was hybridized overnight to Agilent 4x44K Arabidopsis Gene Expression (V4) Microarrays (Agilent G2519F-021169) in an Agilent rotating hybridization oven.

scan_protocol: Arrays were scanned immediately following hybridization with an Agilent G2565B Array Scanner.

data_processing: Images were analyzed using the Feature Extractor v9.5 default protocol GE1-v5_95_Feb07. Quantile normalization was performed on all probes using the “gProcessedSignal” column of the Feature Extractor files.

organism: Arabidopsis thaliana

source_name: Leaf, fumigated, unstressed, 24 hours

label_protocol: Nucleic acid labeling was performed according to Agilent recommended procedures for single-color arrays at the Michigan State University Research Technology Support Facility.

growth_protocol: Plants were grown under a 12 hr photoperiod in 120 µmol m-2 s-1 fluorescent lighting, 60% relative humidity, and a 23/20 °C day-night temperature.

extract_protocol: Total RNA was isolated from single leaves using an RNeasy Plant Mini Kit (Qiagen, Venlo, The Netherlands). An Agilent Bioanalyzer (Agilent, Santa Clara, CA, USA) was used to check RNA quality.

treatment_protocol: Plants were fumigated for 24 hrs in an aluminum gas exchange chamber that was custom-built for use with Arabidopsis rosettes. A 12 hr photoperiod (120 µmol m-2 s-1) was provided by a white LED lamp. A glass window allowed light to penetrate to the rosette. A water bath connected to a water jacket in the base of the gas-exchange chamber maintained the set temperature.

tag: age

value: leaf

tag: treatment

value: 24 hours in 20 ppm isoprene at 23 °C


title: 22a-N,Normal thyroid,N0

source_name: 22a-N,Normal thyroid,N0


title: MW3

source_name: Male_wildtype_Replicate 3

value: Prefrontal cortex striatum

value: adult


title: MW4

source_name: Male_wildtype_Replicate 4


title: Leaf_noISP_40C_rep3

description: Gene expression after 24 hours in 0 ppm isoprene at 40 °C

source_name: Leaf, unfumigated, heat stressed, 24 hours

value: 24 hours in 0 ppm isoprene at 40 °C


title: Leaf_ISP_23C_rep2


title: 9-N,Normal thyroid,N1

source_name: 9-N,Normal thyroid,N1

value: I


title: Leaf_noISP_40C_rep2


title: L4

source_name: low salt

growth_protocol: 8 weeks old C57Bl/6j male mice were subjected for 8 weeks to normal (N, 0.4% Na) or low (L, 0.05%Na) salt diet then sacrificed when 16 weeks old.

treatment_protocol: Mice were anesthetized with pentobarbital sodium (50mg/Kg). After blood was collected, the septum, free wall and apex of the left ventricle were collected and homogenized.

value: heart left ventricle


title: Leaf_ISP_40C_rep1

description: Gene expression after 24 hours in 20 ppm isoprene at 40 °C

source_name: Leaf, fumigated, heat stressed, 24 hours

value: 24 hours in 20 ppm isoprene at 40 °C


title: Leaf_ISP_40C_rep2


title: Leaf_noISP_40C_rep1


title: Leaf_ISP_40C_rep3


title: 23-PT-N0,Papillary thyroid carcinoma,N0

source_name: 23-PT-N0,Papillary thyroid carcinoma,N0

value: F

value: Trabecular

value: no

value: BRAFmut


title: MW1

source_name: Male_wildtype_Replicate 1


title: Leaf_ISP_23C_rep1


title: Leaf_noISP_23C_rep1

description: Gene expression after 24 hours in 0 ppm isoprene at 23 °C

source_name: Leaf, unfumigated, unstressed, 24 hours

value: 24 hours in 0 ppm isoprene at 23 °C


title: acl5-4 ajax2-31 vs acl5-4 replicate 1

city: Valencia

first: Francisco

last: Vera-Sirera

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP (UPV-CSIC)

hyb_protocol: Hybridization and slide washing were carried out with the Gene Expression Hybridization Kit and Gene Expression Wash Buffers, respectively

scan_protocol: Scanned on Agilent Technologies Scanner G2505B at a resolution of 5 microns per pixel,using the double scanning as Agilent’s recommended settings. Images were quantified using Agilent Feature Extraction Software (version 9.5.1)

data_processing:
Inter-array analyses were performed with the GeneSpring 11.5 software. Dye-swap was undo to made all ratio as supressor of acl5/acl5 mutant. To ensure high quality dataset, control features were removed, and only features for which the ‘IsWellAboveBG’ parameter was 1 at least in two out of three replicas were selected in at least one of the four comparations.
Linear and lowess normalized log2 ratio (supressor of acl5/acl5 mutant). Values for Col vs acl5-1 replicate 3, acl5-1 + pHS::SACL3 vs acl5-1 30 min heat shock + 30 min replicate 2, acl5-1 + pHS::SACL3 vs acl5-1 30 min heat shock + 30 min replicate 3, acl5-1 + pHS::SACL3 vs acl5-1 30 min heat shock + 210 min replicate 3 and acl5-4 ajax2-31 vs acl5-4 replicate 3 has been dye-swap corrected.

source_name: acl5-4 ajax2-31 10 days seedlings

label_protocol: 0.5 µg of total RNA 0.5 were amplified and labeled with the Agilent Low Input Quick Amp Labeling Kit. Agilent’s Spike-In Kit was used to assess the labeling and hybridization efficiencies

growth_protocol: Seeds were surface sterilized by a treatment with 70% ethanol +  0.05 % Triton X-100 for 3 min, followed by treatment a with 96% ethanol for 1 min. Once seeds were dried they were  sowed on plates with Murashige-Skoog (MS) solid medium. The two different genotypes that were going to be compared in the same array were also grown in the same plate. Stratification of the seeds was conducted in the dark at 4C for 3 days. Then, seeds were incubated in a controlled environment growth chamber at 22C under a 16 h light, 8 h dark photoperiod at 80-100 µE m-2 sec-1; during 10 days.

extract_protocol: Seedlings were frozen in liquid nitrogen, and grounded in mortars dipped in liquid nitrogen. Total RNA was extracted using the Quiagen Plant RNeasy Mini Kit followong the manufacturer´s recommendations

treatment_protocol: The acl5 + pHS::SACL3 seedlings (and the acl5 ones against they are went compared) were treated to 37C degrees heat shock and then collected at two different times (30 and 210 min) after heat shock.

tag: ecotype/genotype background

value: Ler

tag: genotype/variation

value: acl5-4 ajax2.31

value: seedlings

value: 10 days

source_name: acl5-4 10 days seedlings

value: Seedlings


title: Leaf_noISP_23C_rep2

value: leaf


title: MW2

source_name: Male_wildtype_Replicate 2

value: Male

value: Prefrontal cortex striatum


title: L3

value: adult


title: Leaf_noISP_23C_rep3


title: L2


title: 21a-PT-N0,Papillary thyroid carcinoma,N0

value: M

value: III

value: Papillary

value: left

value: yes


title: acl5-4 ajax2-31 vs acl5-4 replicate 2


title: 18-LNM,Lymph node metastasis,N1

source_name: 18-LNM,Lymph node metastasis,N1

value: F

value: I

value: no


title: acl5-1 + pHS::SACL3 vs acl5-1 30 min heat shock + 210 min replicate 3

source_name: acl5-1 + pHS::SACL3 30 min heat shock + 210 min 10 days seedlings

value: acl5-1 + pHS::SACL3

tag: treated with

value: 30 min heat shock 37ºC

tag: harvest time point

value: 210min after heat shock

source_name: acl5-1 30 min heat shock + 210 min 10 days seedlings


title: 21a-N,Normal thyroid,N0

source_name: 21a-N,Normal thyroid,N0

value: BRAFmut


title: acl5-1 + pHS::SACL3 vs acl5-1 30 min heat shock + 210 min replicate 1

value: seedlings

value: 10 days

value: Seedlings


title: N4

source_name: normal salt

tag: strain

value: Male

value: heart left ventricle


title: L1

value: adult


title: acl5-1 + pHS::SACL3 vs acl5-1 30 min heat shock + 30 min replicate 3

source_name: acl5-1 + pHS::SACL3 30 min heat shock + 30 min 10 days seedlings

value: 30min after heat shock

source_name: acl5-1 30 min heat shock + 30 min 10 days seedlings


title: N3


title: Col vs acl5-1 replicate 1

source_name: Col-0 10 days seedlings

value: wild type

source_name: acl5-1 10 days seedlings


title: 22-PT-N0,Papillary thyroid carcinoma,N0

source_name: 22-PT-N0,Papillary thyroid carcinoma,N0

value: M

value: III

value: Papillary

value: right


title: 8-LNM,Lymph node metastasis,N1

source_name: 8-LNM,Lymph node metastasis,N1

value: I

value: both

value: yes

value: no


title: acl5-1 + pHS::SACL3 vs acl5-1 30 min heat shock + 30 min replicate 2

value: acl5-1 + pHS::SACL3

value: 30 min heat shock 37ºC


title: Col vs acl5-1 replicate 2

value: seedlings

value: 10 days


title: acl5-1 + pHS::SACL3 vs acl5-1 30 min heat shock + 210 min replicate 2

value: 210min after heat shock

value: Seedlings


title: acl5-1 + pHS::SACL3 vs acl5-1 30 min heat shock + 30 min replicate 1


title: 11a-PT-N1,Papillary thyroid carcinoma,N1

value: BRAFmut


title: Col vs acl5-1 replicate 3


title: N1

value: Male

value: heart left ventricle

value: adult


title: 18-N,Normal thyroid,N1

source_name: 18-N,Normal thyroid,N1

value: F

value: left


title: Polysome ratio Mature Leaves rep2.

city: Ikoma

first: Shotaro

last: Yamasaki

state: NARA

address: 8916-5 Takayama

department: Graduate school of bilogical science

country: Japan

institute: Nara institute of science and technology

description: Translational state in more aged three leaves other than cotyledons of 21 day after germination

hyb_protocol: Mixtures of 0.85 μg of Cy3- and Cy5-labeled cRNAs (polysome fraction and total fraction RNAs derived from identical plant cell lysates) were co-hybridized at 65°C for 17 h on an Agilent Technologies 4×44K Arabidopsis 4 60 mer oligo microarray.

scan_protocol: The slide was scanned with an Agilent G2565CA Scanner (Agilent Technologies) at a pixel resolution size of 5 μm to detect fluorescence intensity.

data_processing:
The fluorescent intensity of individual features (spots) on scanned images was quantified and corrected for background signal using Feature Extraction software (Agilent Technologies). We evaluated the reproducibility of the microarray analyses according to the manufacturer’s publication, and only features that passed three criteria were used for further analysis. Features flagged in Feature Extraction software as non-uniform (IsFeatNonUnifOL and IsFeatPopnOL field), saturated (IsSaturated field) or low signal (IsWellAboveBG field) in either of the two biological replicates were omitted. The data were normalized using a Linear and LOWESS method, which is the default method for normalizing Agilent microarrays. Polysomal RNA profiling data were normalized via a Linear and LOWESS method followed by spike-in normalization utilizing a Two-Color RNA Spike-In Kit (Agilent Technologies). As described above, since 10 in vitro synthesized E1A transcripts were added to each fraction in various predetermined ratios concomitantly with the collection of a sucrose gradient, their signal ratios between two fractions can be used to monitor variation in preparation steps such as RNA isolation, reverse transcription, sample amplification, dye labeling or hybridization. Out of 10 spike-in RNAs, two (E1A_r60_1 and E1A_r60_a20 RNAs, whose expected ratios are 1:1) were used for spike-in normalization.
For polysomal RNA profiling, the ratio of the intensity value in the polysome fraction RNA plant cell (Cy3) over that in the total fraction RNA plant cell (Cy5) was calculated, and defined as the translational state or polysome ratio (PR). The average of (Cy3/Cy5) values was calculated for genes mapped on more than two features on an array, and then for the two biological replicates. We also calculated the change in PR values through growth stage (ΔPRgrowth= log10PR21DAG − log10PR2DAG) and leaf development (ΔPRleaf= log10PRmature leaves − log10PRyoung leaves).

source_name: Total RNA, Col-0, mature leaves, 21 day after germination

label_protocol: Fluorescent cRNAs were generated from polysome fraction and total fraction RNAs from each plant cells using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). A 500 ng aliquot of RNA was subjected to reverse transcription using MMLV reverse transcriptase and oligo (dT) primer containing the T7 promoter, and was subsequently in vitro transcribed using T7 RNA polymerase, resulting in Cy3- and Cy5-labeled cRNAs. The cRNAs were purified using RNeasy mini spin columns (Qiagen). Polysome fraction RNAs were labeled with Cy3, and total fraction RNAs were labeled with Cy5.

growth_protocol: The Arabidopsis thaliana ecotype Columbia-0 was surface sterilized, sown on GM medium plates, and kept at 4°C in darkness for 3 days for stratification. The seeds were grown in growth chambers under long-day conditions (16 h light/8 h dark) at 22°C.

extract_protocol: Each plant cells were pulverized with mortar and pestle. The resulting frozen powder was homogenized of buffer U (200 mM Tris-HCl, pH 8.5, 50 mM KCl, 25 mM MgCl2, 2 mM EGTA, 100 μg ml−1 heparin, 100 μg ml−1 cycloheximide, 2% polyoxyethylene 10-tridecyl ether, and 1% sodium deoxycholate) and centrifuged at 15,000×g for 10 min at 4°C. Aliquots of supernatant were layered on 4.85 ml of a 26.25−71.25% sucrose density gradient in buffer B (50 mM Tris-HCl, pH 8.5, 25 mM KCl, and 10 mM MgCl2) and centrifuged at 55,000 r.p.m. for 50 min at 4°C in an SW55 rotor (Beckman Coulter). The gradient was collected from the bottom using a piston gradient fractionator (BioComp Instruments) with simultaneous recording of absorbance profiles at 254 nm using a UV monitor.Fractions 5−8 (polysome fraction) and 1−8 (total fraction) of the eight fractions were individually collected and pooled into tubes containing guanidine hydrochloride (final concentration, 5.5 M) (direction of sedimentation is from fraction 1 to fraction 8). As external controls, 5 μl of Spike A and Spike B Mix (Two-Color RNA Spike-In Kit; Agilent Technologies) were added to the polysome and total fractions, respectively, concomitant with collection of the sucrose gradient. RNA was precipitated from each fraction by the addition of an equal volume of ethanol, overnight incubation at –20°C and centrifugation at 10,000 r.p.m for 45 min in a JA-20 rotor (Beckman Coulter). The resulting precipitate was washed with 80% ethanol. RNA was purified using an RNeasy kit (Qiagen) with on-column DNase I treatment according to the manufacturer’s instructions. RNA was eluted with 30 μl of RNase-free water and eluted RNA solution was further subjected to LiCl precipitation by the addition of LiCl at a final concentration of 1.5 M, followed by centrifugation. After ethanol precipitation, the RNA integrity was examined with an Agilent Bioanalyzer 2100 (Agilent technologies).

value: Mature leaves

value: 21 day after germination

tag: fraction

value: Total RNA [fractions 1−8 (total fraction) of the eight fractions]

source_name: Polysomal RNA, Col-0, mature leaves, 21 day after germination

value: Polysomal RNA [fractions 5−8 (polysome fraction) of the eight fractions]


title: Polysome ratio 21DAG rep1.

description: Translational state in above ground part of 21 day after germination

source_name: Total RNA, Col-0, above ground part, 21 day after germination

value: Above ground part

source_name: Polysomal RNA, Col-0, above ground part, 21 day after germination


title: 8-PT-N1,Papillary thyroid carcinoma,N1

source_name: 8-PT-N1,Papillary thyroid carcinoma,N1

value: M

value: I

value: Papillary

value: both

value: yes

value: no


title: Adult mouse cardiac mesenchymal progenitor with OSKM at D6

city: Kyoto

first: Satoshi

last: Gojo

address: 465 Kajii-cho, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

hyb_protocol: Hybridization and washing steps were performed using Gene Expression Wash Pack (Agilent Technology) according to the manufacturer's instructions.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using DNA MicroArray Scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software version 9.5.3 and further analyzed using GeneSpring GX software version 11.0.2. Data were normalized to the 75th percentile (median).

source_name: Sca-1+ cells from heart, OSKM, day 6

label_protocol: 250 ng of total RNA was labelled with Cy3 using the Low RNA Fluorecent Linear Amplification Kit PLUS, One-Color (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Cardiac mesenchymal progenitors (CMPs) were cultured on Collagen I coated dish in DMEM/F12 supplemented with 10% FBS, 40 ng/ml bFGF.

extract_protocol: Total RNA was extracted from each sample using the TRIzol Reagent (Life technologies, Inc.) and Direct-zol™ RNA MiniPrep Kit (Zymo Research).

tag: strain/background

value: adult cardiac mesenchymal progenitors

value: OKSM

tag: time point

value: day 6


title: N2

value: Male

tag: tissue

value: heart left ventricle

value: adult


title: 27-PT-N0,Papillary thyroid carcinoma,N0

source_name: 27-PT-N0,Papillary thyroid carcinoma,N0

tag: Sex

value: F

value: Follicular

value: left

value: BRAFmut


title: Polysome ratio 21DAG rep2.

value: Above ground part

value: 21 day after germination

value: Total RNA [fractions 1−8 (total fraction) of the eight fractions]

value: Polysomal RNA [fractions 5−8 (polysome fraction) of the eight fractions]


title: 5-N,Normal thyroid,N1

source_name: 5-N,Normal thyroid,N1

value: I


title: 22-N,Normal thyroid,N0

source_name: 22-N,Normal thyroid,N0

value: M

value: III

value: Papillary

value: right

value: yes


title: Polysome ratio Young Leaves rep2.

description: Translational state in newer three leaves of 21 day after germination

source_name: Total RNA, Col-0, young leaves, 21 day after germination

value: Young leaves

source_name: Polysomal RNA, Col-0, young leaves, 21 day after germination


title: Polysome ratio 2DAG rep1.

description: Translational state in whole plants of 2 day after germination

source_name: Total RNA, Col-0, whole plant, 2 day after germination

value: Whole plant

value: 2 day after germination

source_name: Polysomal RNA, Col-0, whole plant, 2 day after germination


title: Adult mouse cardiac mesenchymal progenitor with OSKM at D8

source_name: Sca-1+ cells from heart, OSKM, day 8

tag: cell type

value: adult cardiac mesenchymal progenitors

value: OKSM

value: day 8


title: Polysome ratio Young Leaves rep1.


title: Polysome ratio Mature Leaves rep1.

value: Mature leaves


title: Polysome ratio 2DAG rep2.


title: Adult mouse cardiac mesenchymal progenitor without any treatment

source_name: Sca-1+ cells from heart, untreated

value: day 0


title: Adult mouse cardiac mesenchymal progenitor with OSKM at D4

source_name: Sca-1+ cells from heart, OSKM, day 4

value: day 4


title: Total RNA Young Leaves rep2.

description: Gene expression in newer three leaves of 21 day after germination

hyb_protocol: 1.65 μg of Cy3-labeled cRNAs (total RNAs from each plant cells) were hybridized at 65°C for 17 h on an Agilent Technologies 4×44K Arabidopsis 4 60 mer oligo microarray.

data_processing:
The fluorescent intensity of individual features (spots) on scanned images was quantified and corrected for background signal using Feature Extraction software (Agilent Technologies). We evaluated the reproducibility of the microarray analyses according to the manufacturer’s publication, and only features that passed three criteria were used for further analysis. Features flagged in Feature Extraction software as non-uniform (IsFeatNonUnifOL and IsFeatPopnOL field), saturated (IsSaturated field) or low signal (IsWellAboveBG field) in either of the two biological replicates were omitted. The data were normalized using a Linear and LOWESS method, which is the default method for normalizing Agilent microarrays.
For total RNA profiling, the ratio of the intensity value (expression score) in the 21DAG plant cell over that in the 2DAG plant cell (ES_growth) or in the mature leaves plant cell over that in the young leaves plant cell (ES_leaf) was calculated for features that passed the above criteria.

source_name: Col-0, young leaves, 21 day after germination

label_protocol: Fluorescent cRNAs were generated from total RNAs from each plant cells using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). A 500 ng aliquot of RNA was subjected to reverse transcription using MMLV reverse transcriptase and oligo (dT) primer containing the T7 promoter, and was subsequently in vitro transcribed using T7 RNA polymerase, resulting in Cy3-labeled cRNAs. The cRNAs were purified using RNeasy mini spin columns (Qiagen).

extract_protocol: Each plant cells were pulverized as described above for the polysome fractionation assay. First, total RNA was isolated from the frozen powder using TRIzol Reagent (Invitrogen) followed by RNeasy mini spin columns with on-column DNase I treatment. The reagents and kit were used according to the manufacturer’s instructions. RNA integrity was examined with an Agilent Bioanalyzer 2100 (Agilent Technologies).

value: 21 day after germination


title: 21-PT-N0,Papillary thyroid carcinoma,N0

source_name: 21-PT-N0,Papillary thyroid carcinoma,N0

tag: rqi

value: left

value: no

value: BRAFmut


title: Total RNA 21DAG rep2.

description: Gene expression in above ground part of 21 day after germination

source_name: Col-0, above ground part, 21 day after germination

value: Above ground part


title: Total RNA Mature Leaves rep2.

description: Gene expression in more aged three leaves other than cotyledons of 21 day after germination

source_name: Col-0, mature leaves, 21 day after germination


title: Total RNA 21DAG rep1.


title: 4-R,Recurrence,N1

value: M

tag: tnm

value: IVA

value: Papillary


title: Total RNA Young Leaves rep1.

value: Young leaves


title: Total RNA Mature Leaves rep1.


title: MEF, eIF2a A/A, Tun rep2

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Division of Molecular Biology

institute: Institute for Genome Research

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent Fragmentation buffer and 1x Agilent Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17.5 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air-dried immediately.

scan_protocol: Slides were scanned immediately after washing and drying on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%, NoXDR setting).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20100422) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MEF, eIF2a A/A, Tun rep2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the Low Input Quick Amp Labeling Kit (One-Color) (Agilent) according to the manufacturer's instructions, followed by RNeasy mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: MEFs were cultured in DMEM supplemented with 10% fetal bovine serum, 55uM 2-mercaptoethanol, 1x MEM non-essential amino acids, 100units/ml penicillin and 100ug/ml streptomycin at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: total RNA was prepared using the mirVana miRNA Isolation Kit (Ambion, Life Technologies, Carlsbad, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored by agarose gel electrophoresis of RNA under denaturing conditions.

treatment_protocol: MEFs were treated with DMEM supplemented with 10% fetal bovine serum, 55uM 2-mercaptoethanol, 1x MEM non-essential amino acids, 100units/ml penicillin and 100ug/ml streptomycin containing 2ug/mL tunicamycin for 12 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: Mouse Embryonic Fibroblast (MEF)

tag: genotype

value: eIF2a A/A

value: Tun 12h


title: MEF, eIF2a A/A, Tun rep1

source_name: MEF, eIF2a A/A, Tun rep1


title: Total RNA 2DAG rep2.

description: Gene expression in whole plants of 2 day after germination

source_name: Col-0, whole plant, 2 day after germination

value: Whole plant

value: 2 day after germination


title: 2-NLN,Normal lymph node,N1

source_name: 2-NLN,Normal lymph node,N1

value: F

tag: Stage

value: III

value: right

tag: multifocal

value: yes

value: 5 on 7


title: Total RNA 2DAG rep1.

tag: age


title: acl5-4 ajax2-31 vs acl5-4 replicate 3

source_name: acl5-4 ajax2-31 10 days seedlings

tag: ecotype/genotype background

value: Ler

value: acl5-4 ajax2.31

value: seedlings

value: 10 days

source_name: acl5-4 10 days seedlings

value: Seedlings


title: 8-N,Normal thyroid,N1

source_name: 8-N,Normal thyroid,N1

value: M

value: I

value: Papillary

value: both

value: no

value: BRAFmut


title: 27-N,Normal thyroid,N0

source_name: 27-N,Normal thyroid,N0

value: Follicular

value: left


title: MEF, eIF2a A/A, UT rep1

source_name: MEF, eIF2a A/A, UT rep1

value: Mouse Embryonic Fibroblast (MEF)

value: eIF2a A/A

tag: treatment

value: Untreated


title: 2-LNM,Lymph node metastasis,N1

source_name: 2-LNM,Lymph node metastasis,N1

value: F

value: III

value: right

value: yes

value: 5 on 7


title: MEF, eIF2a A/A, UT rep2

source_name: MEF, eIF2a A/A, UT rep2


title: Head and neck squamous cell carcinomas cell line_93VU

city: chicago

first: Tanguy

last: Seiwert

state: IL

address: 900 E. 57th street

institute: University of Chicago

description: gene expression profile on HNSCC cell lines

hyb_protocol: Expression arrays were performed at the Argonne National Laboratory in an ozone-controlled atmosphere.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1. Raw data were background corrected, quantile normalized and log2 transformed. The control probes were removed.

label_protocol: Labeling for Agilent 4x44K expression arrays was done using a Quick Amp Labeling Kit one-color according to the manufacturer’s protocol using 200ng of starting material.

extract_protocol: Guided by H&E stained slides, the region with the highest tumor content was cut from OCT blocks, pulverized using CryoPrep (Covaris, Woburn, MA) and homogenized in a lysis buffer from an AllPrepRNA/DNA/Protein Mini kit (Qiagen, Valencia, CA) or from a RNA/DNA/Protein Purification Kit (Norgen Biotek, Thorold, Canada) using an Ultrasonicator (Covaris, Woburn, MA). DNA, RNA and protein were isolated from each sample using the respective kit and following manufacturer’s protocol. RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). If DNA contamination was seen, RNAs were treated with TURBO DNA-free (Ambion, CA) to remove genomic DNA, and subsequently quantitated using a spectrophotometer. Only RNAs with integrity number (RIN) ≥7.5, a 260/280 ratio ≥1.8 and a 260/230 ratio ≥1.8 (≥1.1 for a few RNAs) were labeled for expression arrays.

tag: cell line

tag: hpv status

value: positive


title: Head and neck squamous cell carcinomas cell line_SCC35

value: negative


title: 21-N,Normal thyroid,N0

source_name: 21-N,Normal thyroid,N0

value: M


title: Head and neck squamous cell carcinomas cell line_SCC2


title: Head and neck squamous cell carcinomas cell line_SCC166


title: MEF, Tg(Fv2E-PERK), AP, rep2

source_name: MEF, Tg(Fv2E-PERK), AP, rep2

value: AP 12h


title: 4-N,Normal thyroid,N1

source_name: 4-N,Normal thyroid,N1

value: IVA

value: Papillary


title: MEF, Tg(Fv2E-PERK), UT, rep1

source_name: MEF, Tg(Fv2E-PERK), UT, rep1


title: Head and neck squamous cell carcinomas cell line_DOK

value: DOK


title: Head and neck squamous cell carcinomas cell line_HN5


title: Hela cell line_OSCC3

source_name: Hela cell line


title: Head and neck squamous cell carcinomas cell line_SCC90


title: 2-PT-N1,Papillary thyroid carcinoma,N1

source_name: 2-PT-N1,Papillary thyroid carcinoma,N1

value: no


title: MEF, Tg(Fv2E-PERK), UT, rep2

source_name: MEF, Tg(Fv2E-PERK), UT, rep2


title: Head and neck squamous cell carcinomas cell line_SCC25


title: Head and neck squamous cell carcinomas cell line_SCC4


title: MEF, ATF4KO, Tun, rep1

source_name: MEF, ATF4KO, Tun, rep1

value: Tun 12h


title: Head and neck squamous cell carcinomas cell line_PJ49


title: MEF, ATF4KO, Tun, rep2

source_name: MEF, ATF4KO, Tun, rep2

value: Mouse Embryonic Fibroblast (MEF)


title: Head and neck squamous cell carcinomas cell line_SCC9


title: MEF, ATF4KO, UT, rep2

source_name: MEF, ATF4KO, UT, rep2


title: 7-PT-N1,Papillary thyroid carcinoma,N1

source_name: 7-PT-N1,Papillary thyroid carcinoma,N1

value: I

value: left


title: 16-PLM,Pleural metastasis,N1

source_name: 16-PLM,Pleural metastasis,N1

value: IVC

value: poorly differentiated with well differentiated PTC compatible areas

value: NRAS


title: MEF, ATF4KO, UT, rep1

source_name: MEF, ATF4KO, UT, rep1

value: Untreated


title: Head and neck squamous cell carcinomas cell line_CAL27


title: Head and neck squamous cell carcinomas cell line_H400


title: Head and neck squamous cell carcinomas cell line_JSQ3


title: Head and neck squamous cell carcinomas cell line_SCC151


title: Head and neck squamous cell carcinomas cell line_SCC135


title: Head and neck squamous cell carcinomas cell line_PJ15


title: MEF, PERKKO, Tun, rep2

source_name: MEF, PERKKO, Tun, rep2

value: PERKKO


title: 26-PT-N0,Papillary thyroid carcinoma,N0

source_name: 26-PT-N0,Papillary thyroid carcinoma,N0

value: III

value: right

value: yes

value: BRAFmut


title: Head and neck squamous cell carcinomas cell line_SCC47

value: positive


title: 3-N,Normal thyroid,N1

source_name: 3-N,Normal thyroid,N1

value: F

value: Papillary

value: both


title: MEF, PERKKO, Tun, rep1

source_name: MEF, PERKKO, Tun, rep1

value: Tun 12h


title: Head and neck squamous cell carcinomas cell line_H357

value: negative


title: 16-LNM1,Lymph node metastasis,N1

source_name: 16-LNM1,Lymph node metastasis,N1

value: M

value: no


title: MEF, PERKKO, UT, rep2

source_name: MEF, PERKKO, UT, rep2

value: Mouse Embryonic Fibroblast (MEF)


title: Head and neck squamous cell carcinomas cell line_DETROIT

value: DETROIT


title: Head and neck squamous cell carcinomas cell line_SAS

value: SAS


title: MEF, PERKKO, UT, rep1

source_name: MEF, PERKKO, UT, rep1

value: Untreated


title: Head and neck squamous cell carcinomas cell line_HN13


title: 6-LNM,Lymph node metastasis,N1

source_name: 6-LNM,Lymph node metastasis,N1

value: I

value: Tubulair


title: Head and neck squamous cell carcinomas cell line_SCC61


title: Head and neck squamous cell carcinomas cell line_1483


title: Head and neck squamous cell carcinomas cell line_SCC15


title: 6-PT-N1,Papillary thyroid carcinoma,N1

source_name: 6-PT-N1,Papillary thyroid carcinoma,N1


title: Head and neck squamous cell carcinomas cell line_HN6


title: Head and neck squamous cell carcinomas cell line_SCC294


title: Head and neck squamous cell carcinomas cell line_SCC23


title: Head and neck squamous cell carcinomas cell line_BICR22


title: Head and neck squamous cell carcinomas cell line_HN4


title: 11-N,Normal thyroid,N1

source_name: 11-N,Normal thyroid,N1


title: 16-PT-N1,Papillary thyroid carcinoma,N1

source_name: 16-PT-N1,Papillary thyroid carcinoma,N1

value: IVC

value: poorly differentiated with well differentiated PTC compatible areas

value: right

value: NRAS


title: Head and neck squamous cell carcinomas cell line_SQ38


title: 16-LNM2,Lymph node metastasis,N1

source_name: 16-LNM2,Lymph node metastasis,N1

value: yes


title: Head and neck squamous cell carcinomas cell line_SCC58


title: MEF, Tg(Fv2E-PERK), AP, rep1

source_name: MEF, Tg(Fv2E-PERK), AP, rep1

value: AP 12h


title: Head and neck squamous cell carcinomas cell line_OECM.1


title: MEF, WT, Tun, rep3

source_name: MEF, WT, Tun, rep3

value: Wild Type


title: MEF, WT, Tun, rep2

source_name: MEF, WT, Tun, rep2

value: Tun 12h


title: MEF, WT, Tun, rep4

source_name: MEF, WT, Tun, rep4


title: 5-LNM,Lymph node metastasis,N1

source_name: 5-LNM,Lymph node metastasis,N1

value: F

value: Follicular

value: left


title: Head and neck squamous cell carcinomas cell line_MSK921

value: negative


title: Head and neck squamous cell carcinomas cell line_SCC68


title: 7-LNM,Lymph node metastasis,N1

source_name: 7-LNM,Lymph node metastasis,N1

value: Papillary

value: no


title: 5-PT-N1,Papillary thyroid carcinoma,N1

source_name: 5-PT-N1,Papillary thyroid carcinoma,N1


title: 7-N,Normal thyroid,N1

source_name: 7-N,Normal thyroid,N1


title: 26-N,Normal thyroid,N0

source_name: 26-N,Normal thyroid,N0

value: M

value: III

value: BRAFmut


title: 11-LNM1,Lymph node metastasis,N1

source_name: 11-LNM1,Lymph node metastasis,N1

value: I

value: both


title: Head and neck squamous cell carcinomas cell line_H103


title: MEF, WT, UT, rep4

source_name: MEF, WT, UT, rep4

value: Mouse Embryonic Fibroblast (MEF)

value: Untreated


title: 1-LNM,Lymph node metastasis,N1

source_name: 1-LNM,Lymph node metastasis,N1

value: yes

value: 8 on 8


title: 3-NLN,Normal lymph node,N1

source_name: 3-NLN,Normal lymph node,N1


title: 3-LNM,Lymph node metastasis,N1

source_name: 3-LNM,Lymph node metastasis,N1


title: 29-PT-N0,Papillary thyroid carcinoma,N0

source_name: 29-PT-N0,Papillary thyroid carcinoma,N0

value: right


title: Head and neck squamous cell carcinomas cell line_BiCR31


title: 11-LNM2,Lymph node metastasis,N1

source_name: 11-LNM2,Lymph node metastasis,N1


title: 4-LNM,Lymph node metastasis,N1

source_name: 4-LNM,Lymph node metastasis,N1

value: IVA


title: 4-PT-N1,Papillary thyroid carcinoma,N1

source_name: 4-PT-N1,Papillary thyroid carcinoma,N1


title: MEF, WT, UT, rep2

source_name: MEF, WT, UT, rep2

value: Wild Type


title: 11-PT-N1,Papillary thyroid carcinoma,N1

source_name: 11-PT-N1,Papillary thyroid carcinoma,N1


title: MEF, WT, UT, rep3

source_name: MEF, WT, UT, rep3


title: Head and neck squamous cell carcinomas cell line_BiCR16


title: 4-NLN,Normal lymph node,N1

source_name: 4-NLN,Normal lymph node,N1


title: Head and neck squamous cell carcinomas cell line_SQ20B


title: MEF, WT, UT, rep1

source_name: MEF, WT, UT, rep1


title: 29-N,Normal thyroid,N0

source_name: 29-N,Normal thyroid,N0

value: F

value: Follicular


title: DLE224 Diseased Skin

city: Dallas

first: Benjamin

last: Chong

address: 6000 Harry Hines Blvd

department: Dermatology

institute: University of Texas Southwestern

description:
8381645021_L
Diseased Skin

hyb_protocol: Biotin labeled cRNA are hybridized with Illumina Rat-Ref-12-V1 Beadchips using Illumina standard protocol

scan_protocol: The beadchips are scanned using Illumina HiScan scanner

data_processing: The data is analyzed using Illumina GenomeStudio software

source_name: Human Skin

label_protocol: The RNA samples are labeled with Biotin using Illumina TotalPrep RNA Amplification Kit

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: disease status

value: discoid lupus lesional


title: DLE223 Diseased Skin

description:
8381645021_J
Diseased Skin


title: NL345 Normal Skin

description:
8381645021_K
Normal Skin

value: normal


title: NL344 Normal Skin

description:
8381645021_I
Normal Skin


title: 17-LNM,Lymph node metastasis,N1

source_name: 17-LNM,Lymph node metastasis,N1

value: Papillary

value: no

value: 1 on 6


title: DLE226A Diseased Skin

description:
8381645021_H
Diseased Skin


title: DLE47(3) Diseased Skin

description:
8381645016_K
Diseased Skin


title: 28-PT-N0,Papillary thyroid carcinoma,N0

source_name: 28-PT-N0,Papillary thyroid carcinoma,N0

value: BRAFmut


title: DLE60A Diseased Skin

description:
8381645021_G
Diseased Skin


title: DLE250 Diseased Skin

description:
8381645016_J
Diseased Skin


title: NL334 Normal Skin

description:
8381645016_F
Normal Skin


title: DLE258A Diseased Skin

description:
8381645016_H
Diseased Skin


title: DLE254A Diseased Skin

description:
8381645016_I
Diseased Skin


title: 28-N,Normal thyroid,N0

source_name: 28-N,Normal thyroid,N0

value: I


title: 20-NLN,Normal lymph node,N0

source_name: 20-NLN,Normal lymph node,N0

value: M


title: 25-PT-N0,Papillary thyroid carcinoma,N0

source_name: 25-PT-N0,Papillary thyroid carcinoma,N0

value: left


title: 19-LNM,Lymph node metastasis,N1

source_name: 19-LNM,Lymph node metastasis,N1

value: both


title: NL336A Normal Skin

description:
8381645016_E
Normal Skin


title: NL335 Normal Skin

description:
8381645016_B
Normal Skin


title: NL337 Normal Skin

description:
8381645016_A
Normal Skin


title: NL342 Normal Skin

description:
8381645016_C
Normal Skin


title: DLE230 Diseased Skin

description:
8381645016_G
Diseased Skin


title: NL332 Normal Skin

description:
8381645016_D
Normal Skin


title: 3-PT-N1,Papillary thyroid carcinoma,N1

source_name: 3-PT-N1,Papillary thyroid carcinoma,N1

value: yes


title: LCC2 Control

city: Edinburgh

first: Carlos

last: Martinez-Perez

address: Western General Hospital, Crewe Road South

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: The University of Edinburgh

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi in R

source_name: MCF7-derived Breast Cancer Cell Line

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit for Illumina arrays

growth_protocol: MCF7 and MDA-MB-231: Cells were grown in DMEM supplemented with 10% heat-inactivated FCS and 100IU/ml penicillin/streptomycin, LCC1/2/9: Cells were grown in phenol red free DMEM supplemented with 5% heat inactivated FCS charcoal-stripped of steroids.

extract_protocol: RNA was extracted from flash-frozen pellets of approximately 3 million cells with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser

treatment_protocol: Treated cells were subjected to 6 hours of 10µM OncamexTM in a final vehicle concentration of 1% DMSO.

tag: origin

value: derived from LCC1 selected for tamoxfien resistance

tag: hormone

value: estrogen receptor positive, estrogen independent, tamoxifen resistant

value: 2hrs 1% DMSO


title: LCC9 Control

value: derived from LCC1 selected for fulvestrant resistance

value: estrogen receptor positive, estrogen independent, tamoxifen and fulvestrant resistant


title: LCC9 Treated

value: 6hrs 10µM OncamexTM


title: 10-LNM,Lymph node metastasis,N1

source_name: 10-LNM,Lymph node metastasis,N1

value: F


title: LCC1 Control

value: dervied from MCF7 selected for estrogen independence

value: estrogen receptor positive, estrogen independent, tamoxifen sensitive


title: LCC1 Treated


title: 19-N2,Normal thyroid,N1

source_name: 19-N2,Normal thyroid,N1

value: Papillary

value: no


title: MDA-MB-231 Treated

source_name: MDA-MB-231 Breast Cancer Cell Line

value: human breast epithelial cells derived from metestatic plueral effusion

value: triple (ER, PR, HER2) negative


title: 23a-PT-N0,Papillary thyroid carcinoma,N0

value: III

value: Trabecular

value: right

value: BRAFmut


title: MCF7 Treated

source_name: MCF7 Breast Cancer Cell Line

value: human breast epithelial adenocarcinoma cells

value: estrogen receptor positive, estrogen dependent


title: MCF7 Control

value: 2hrs 1% DMSO


title: MDA-MB-231 Control


title: 25-N,Normal thyroid,N0

source_name: 25-N,Normal thyroid,N0

value: I

value: Follicular

value: left

value: yes


title: 1a-LNM,Lymph node metastasis,N1

source_name: 1a-LNM,Lymph node metastasis,N1

value: M

value: 8 on 8


title: Dovitinib resistance cell rep1

city: Seoul

first: Kyoung-Ho

last: Pyo

address: 50 Yonseiro

department: Avison Biomedical Research Center

country: South Korea

institute: Severance Hospital, Yonsei University College of Medicine

description: Total RNA was amplified and purified using Target Amp-Nano Labeling Kit for Illumina Expression Bead Chip (EPICENTRE) to yield biotinylated cRNA according to the manufacturer’s instructions.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: LC-2/ad-DR cells

extract_protocol: Total RNA was extracted using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol


title: 13-PT-N1,Papillary thyroid carcinoma,N1

source_name: 13-PT-N1,Papillary thyroid carcinoma,N1

value: IVA

value: Papillary

value: both

value: 9 on 9


title: Dovitinib resistance cell rep2

label_protocol: Total RNA was amplified and purified using Target Amp-Nano Labeling Kit for Illumina Expression Bead Chip (EPICENTRE) to yield biotinylated cRNA according to the manufacturer’s instructions


title: HPF_IL6_3

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description:
human prostate fibroblasts IL6
6116768102_K

hyb_protocol: One μg of the biotinylated cRNA was mixed with the Hyb E1 hybridization buffer and then hybridized at 58 °C overnight

scan_protocol: scanned with the Illumina BeadArray Reader according to manufacturer protocol

data_processing: data were log2 transformed and normalized using the Robust Spline Normalization algorithm

source_name: patient-derived fibroblasts

label_protocol: 800 ng of total RNA were reverse transcribed, labeled with biotin and amplified overnight using the Illumina RNA TotalPrep Amplification kit according to manufacturer’s protocol

growth_protocol: Human prostate fibroblasts, HPFs and CAFs, were isolated from healthy and intratumoral regions, respectively, of the prostate of PCa-bearing patients. Tissues were digested overnight in DMEM supplemented with 5% fetal bovine serum and 1X Collagenase-Hyaluronidase Solution (STEMCELLTM Technologies Inc.). Cell suspension was centrifuged at 1,500 g for 5 minutes. The resulting fibroblast-rich pellet was suspended and plated in DMEM containing 10% fetal bovine serum and 4 mM L-Glutammine.

extract_protocol: Total RNA from cells was extracted using TRIzol® reagent (Life Technologies), according to the manufacturer’s instructions.

treatment_protocol: HPFs were grown to sub-confluence and treated for 48 h with 10 ng/ml rTGFβ1 or 50 ng/ml IL6.

value: prostate fibroblasts IL6

tag: replicate


title: 19-N1,Normal thyroid,N1

source_name: 19-N1,Normal thyroid,N1

value: F

value: no

value: 1 on 6


title: Control rep3

source_name: LC-2/ad cells


title: HPF_TGFbeta_3

description:
human prostate fibroblasts TGFb
6116768102_J

value: prostate fibroblasts TGFb

value: TGFbeta


title: CAF__3

description:
cancer associated fibroblasts
6116768102_L

value: cancer associated fibroblasts


title: LCC2 Treated

value: derived from LCC1 selected for tamoxfien resistance

value: estrogen receptor positive, estrogen independent, tamoxifen resistant

value: 6hrs 10µM OncamexTM


title: 13-LNM,Lymph node metastasis,N1

source_name: 13-LNM,Lymph node metastasis,N1

value: yes

value: BRAFmut


title: Control rep2


title: HPF__3

description:
human prostate fibroblasts
6116768102_I

value: prostate fibroblasts


title: 10-PT-N1,Papillary thyroid carcinoma,N1

source_name: 10-PT-N1,Papillary thyroid carcinoma,N1

value: I

value: left


title: Control rep1


title: 13-N,Normal thyroid,N1

source_name: 13-N,Normal thyroid,N1

value: M

value: IVA

value: Papillary

value: both


title: 12-N,Normal thyroid,N1

source_name: 12-N,Normal thyroid,N1

value: F

value: right

value: no

value: 4 on 8


title: HPF_IL6_1

description:
human prostate fibroblasts IL6
6116768102_C

value: prostate fibroblasts IL6


title: 12-LNM,Lymph node metastasis,N1

source_name: 12-LNM,Lymph node metastasis,N1


title: HPF_IL6_2

description:
human prostate fibroblasts IL6
6116768102_G


title: 12-PT-N1,Papillary thyroid carcinoma,N1

source_name: 12-PT-N1,Papillary thyroid carcinoma,N1


title: HPF_TGFbeta_2

description:
human prostate fibroblasts TGFb
6116768102_F

value: prostate fibroblasts TGFb

value: TGFbeta


title: 10-N,Normal thyroid,N1

source_name: 10-N,Normal thyroid,N1


title: Older_Adult_Listeria_6h_subj6

city: Vancouver

first: Kathleen

last: Wee

state: BC

address: 938 W 28th Ave.

country: Canada

institute: University of British Columbia

description:
Older Adult subject 6
8381661062_L

data_processing: The data were normalized using quantile normalization with no background subtraction using Illumina's GenomeStudio software version 1.9.0

source_name: Peripheral blood

label_protocol: Biotinylated cRNA were prepared with the Epicentre's TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit with in-column DNAseI treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: age group

value: Older Adult

value: monocytes

value: Listeria

tag: time


title: CAF__1

description:
cancer associated fibroblasts
6116768102_D

tag: cell type

value: cancer associated fibroblasts


title: HPF__1

description:
human prostate fibroblasts
6116768102_A

value: prostate fibroblasts


title: Older_Adult_Listeria_6h_subj4

description:
Older Adult subject 4
8381661051_D


title: 1a-PT-N1,Papillary thyroid carcinoma,N1

source_name: 1a-PT-N1,Papillary thyroid carcinoma,N1

tag: rqi

tag: Sex

value: I

value: left

value: yes

value: 8 on 8


title: Older_Adult_Listeria_6h_subj5

description:
Older Adult subject 5
8381661062_H


title: Older_Adult_Listeria_6h_subj3

description:
Older Adult subject 3
7680504080_L


title: 23a-N,Normal thyroid,N0

source_name: 23a-N,Normal thyroid,N0

tag: tnm

value: III

value: Trabecular

value: BRAFmut


title: HPF__2

description:
human prostate fibroblasts
6116768102_E


title: 24-PT-N0,Papillary thyroid carcinoma,N0

source_name: 24-PT-N0,Papillary thyroid carcinoma,N0

value: F

tag: Stage

value: no


title: Older_Adult_Listeria_6h_subj2

description:
Older Adult subject 2
7680504080_H


title: Older_Adult_Listeria_6h_subj1

description:
Older Adult subject 1
6334167287_L


title: 9-LNM,Lymph node metastasis,N1

source_name: 9-LNM,Lymph node metastasis,N1

value: M

value: Papillary

value: right

tag: multifocal


title: Older_Adult_unstim_6h_subj5

description:
Older Adult subject 5
8381661062_G

value: Older Adult

value: unstimulated


title: Older_Adult_unstim_6h_subj6

description:
Older Adult subject 6
8381661062_K

value: monocytes


title: Older_Adult_unstim_6h_subj4

description:
Older Adult subject 4
8381661051_C


title: Older_Adult_unstim_6h_subj3

description:
Older Adult subject 3
7680504080_K


title: Skeletal Muscle Sample 19

city: Iowa City

first: Richard

last: Shields

address: 1-252 Medical Education Building

institute: The University of Iowa

description: RMA expression value derived from Partek Genomic Suites

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer and placed onto Affymetrix Human Exon 1.0 ST arrays. Hybridizations were performed by the DNA Core Facility at the University of Iowa.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the GeneChip operating software (GCOS) v1.4.

data_processing: Arrays were normalized using a Robust Multi-array Average (RMA) and transformed into a log2 hybridization signal using Partek Genomic Suites (v6.6 Copyright © 2013 Partek Inc., St. Louis, MO, USA).

source_name: skeletal muscle, trained, experimental

label_protocol: 5μg of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

extract_protocol: Following harvest, muscle biopsy samples were immediately placed In RNALater (Ambion) and stored at -80 C until further use. Total RNA was extracted using TRIzol solution (Invitrogen) according to the manufacturer’s instructions. 50 ng of RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN MinElute Reaction Cleanup column (QIAGEN Cat #28204) according to modifications from NuGEN. Four μg of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.

treatment_protocol: Subjects either received a single unilateral session of exercise 3 hours before a muscle biopsy or subjects unilaterally trained one limb with exercise.

value: trained, experimental

tag: tissue

value: skeletal muscle

tag: gender

value: male


title: Older_Adult_unstim_6h_subj1

description:
Older Adult subject 1
6334167287_K

tag: treatment


title: CD4+CD8+CD71+FSClo thymic T cells from Caph2nes/nes mice_6

first: Andrew

middle: James

last: Wood

address: Crewe Road

institute: University of Edinburgh

description:
Replicate 3
Nes_71+_3

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Raw data were analysed using Bioconductor within the FlexArray software package (http://genomequebec.mcgill.ca/FlexArray). RMA background adjustment, variance stabilisation transformation (VST) and robust spline normalisation were applied. Mean signal values were calculated at the gene level using ANOVA, and tests for difference between sample types were conducted using equal variance T-tests.

source_name: 8 - 12 week thymus

label_protocol: 80ng of total RNA was amplified and biotin-labelled using the Ambion MessageAmp II kit, according to manufacturer's instructions.

growth_protocol: Mice were housed in IVC cages in the Biological Research Facility, Western General Hospital, Edinburgh

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

tag: genotype

tag: strain

value: thymus

tag: age

value: 8-12 week

value: 50/50 mixed male/female


title: Older_Adult_unstim_6h_subj2

description:
Older Adult subject 2
7680504080_G


title: Older_Adult_Listeria_2h_subj5

description:
Older Adult subject 5
8381661062_F

value: Listeria


title: Skeletal Muscle Sample 18

source_name: skeletal muscle, trained, control

value: trained, control


title: Older_Adult_unstim_2h_subj6

description:
Older Adult subject 6
8381661062_I


title: 1-PT-N1,Papillary thyroid carcinoma,N1

source_name: 1-PT-N1,Papillary thyroid carcinoma,N1

value: I

value: left

value: yes

value: 8 on 8


title: CD4+CD8+CD71+FSClo thymic T cells from Caph2nes/nes mice_4

description:
Replicate 1
Nes_71+_1


title: Older_Adult_Listeria_2h_subj6

description:
Older Adult subject 6
8381661062_J


title: CD4+CD8+CD71+FSClo thymic T cells from Caph2nes/nes mice_5

description:
Replicate 2
Nes_71+_2


title: Older_Adult_unstim_2h_subj4

description:
Older Adult subject 4
8381661051_A


title: Older_Adult_Listeria_2h_subj3

description:
Older Adult subject 3
7680504080_J


title: Skeletal Muscle Sample 20


title: CD4+CD8+CD71-FSClo thymic T cells from Caph2nes/nes mice_3

description:
Replicate 3
Nes_71-_3


title: MEF, WT, Tun, rep1

source_name: MEF, WT, Tun, rep1

value: Mouse Embryonic Fibroblast (MEF)

value: Wild Type

value: Tun 12h


title: Older_Adult_unstim_2h_subj3

description:
Older Adult subject 3
7680504080_I

value: Older Adult

value: unstimulated


title: Older_Adult_Listeria_2h_subj2

description:
Older Adult subject 2
7680504080_F

value: monocytes


title: Older_Adult_Listeria_2h_subj4

description:
Older Adult subject 4
8381661051_B


title: CD4+CD8+CD71-FSClo thymic T cells from Caph2nes/nes mice_1

description:
Replicate 1
Nes_71-_1


title: Skeletal Muscle Sample 17

value: skeletal muscle


title: 23-N,Normal thyroid,N0

source_name: 23-N,Normal thyroid,N0

value: F

value: III

value: Trabecular

value: right

value: no

value: BRAFmut


title: Older_Adult_unstim_2h_subj2

description:
Older Adult subject 2
7680504080_E


title: CD4+CD8+CD71-FSClo thymic T cells from Caph2nes/nes mice_2

description:
Replicate 2
Nes_71-_2

value: thymus

value: 8-12 week

value: 50/50 mixed male/female


title: Skeletal Muscle Sample 16

value: trained, experimental

value: male


title: HPF_TGFbeta_1

description:
human prostate fibroblasts TGFb
6116768102_B

source_name: patient-derived fibroblasts

value: prostate fibroblasts TGFb

value: TGFbeta


title: Older_Adult_Listeria_2h_subj1

description:
Older Adult subject 1
6334167287_J

value: Older Adult

value: Listeria


title: Older_Adult_unstim_2h_subj5

description:
Older Adult subject 5
8381661062_E

value: monocytes

value: unstimulated


title: Neonate_Listeria_6h_subj6

description:
Neonate subject 6
8381661062_D

source_name: Cord blood

value: Neonate


title: Skeletal Muscle Sample 15

value: skeletal muscle


title: CD4+CD8+CD71+FSClo thymic T cells from Caph2+/+ mice_6

description:
Replicate 3
WT_71+_3


title: Skeletal Muscle Sample 14

value: trained, control


title: Skeletal Muscle Sample 13


title: Skeletal Muscle Sample 12

source_name: skeletal muscle, acute, experimental

value: acute, experimental


title: CD4+CD8+CD71-FSClo thymic T cells from Caph2+/+ mice_3

description:
Replicate 3
WT_71-_3


title: Skeletal Muscle Sample 11


title: Older_Adult_unstim_2h_subj1

description:
Older Adult subject 1
6334167287_I


title: Neonate_Listeria_6h_subj4

description:
Neonate subject 4
8381661051_H


title: Dovitinib resistance cell rep3

source_name: LC-2/ad-DR cells

tag: cell line


title: Skeletal Muscle Sample 10

source_name: skeletal muscle, acute, control

value: acute, control


title: Neonate_Listeria_6h_subj2

description:
Neonate subject 2
7677161016_L


title: Neonate_Listeria_6h_subj1

description:
Neonate subject 1
6334167287_H


title: CAF__2

description:
cancer associated fibroblasts
6116768102_H

value: cancer associated fibroblasts


title: Neonate_Listeria_6h_subj3

description:
Neonate subject 3
7680504080_D


title: CD4+CD8+CD71-FSClo thymic T cells from Caph2+/+ mice_1

description:
Replicate 1
WT_71-_1

value: thymus


title: Neonate_unstim_6h_subj6

description:
Neonate subject 6
8381661062_C


title: Neonate_Listeria_6h_subj5

description:
Neonate subject 5
8381661051_L


title: CD4+CD8+CD71+FSClo thymic T cells from Caph2+/+ mice_4

description:
Replicate 1
WT_71+_1

value: 8-12 week


title: Neonate_unstim_6h_subj5

description:
Neonate subject 5
8381661051_K


title: Neonate_unstim_6h_subj4

description:
Neonate subject 4
8381661051_G


title: Neonate_unstim_6h_subj1

description:
Adult subject 1
6334167287_G


title: Skeletal Muscle Sample 9


title: CD4+CD8+CD71+FSClo thymic T cells from Caph2+/+ mice_5

description:
Replicate 2
WT_71+_2

value: 50/50 mixed male/female


title: Neonate_unstim_6h_subj2

description:
Adult subject 1
7677161016_K


title: Neonate_unstim_6h_subj3

description:
Adult subject 1
7680504080_C


title: CD4+CD8+CD71-FSClo thymic T cells from Caph2+/+ mice_2

description:
Replicate 2
WT_71-_2


title: Neonate_Listeria_2h_subj6

description:
Neonate subject 6
8381661062_B


title: 19349-2m Liver Tumor

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: The hybridization cocktail containing the Biotin labeled microRNAs was hybridized to the Affymetrix GeneChip® miRNA 3.0 Arrays. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Expression intensities were calculated using GeneChip® Command Console® Software (AGCC version 4.1.2) and Expression Console™ Software (version 1.3.1).

source_name: Liver

label_protocol: Per RNA labeling, 500 nanograms  of total RNA (including small RNAs) was used in conjunction with the Affymetrix recommended protocol Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kits (Cat#901911).

extract_protocol: Total RNAs from liver tissues (including small and long RNAs) was extracted using miRNeasy Mini kit (Qiagen). (cat. no. 217004)

treatment_protocol: All animals received a postnatal AAV-mediated insertional mutagenesis and adult liver was porcessed for whole genome expression analysis.

tag: source

value: Adult liver

value: liver tumor tissue

tag: disease causing mutation

value: AAV-mediated insertional mutagenesis

value: mixed strain of FVB/NJ, C57BL/6, and 129/Sv


title: Skeletal Muscle Sample 8

value: male


title: Neonate_Listeria_2h_subj5

description:
Neonate subject 5
8381661051_J

tag: age group

value: Listeria


title: MS0906531 32856-4f -/- Liver Tumor


title: Neonate_Listeria_2h_subj4

description:
Neonate subject 4
8381661051_F

value: monocytes

tag: time


title: Skeletal Muscle Sample 6


title: Skeletal Muscle Sample 7


title: Neonate_Listeria_2h_subj1

description:
Neonate subject 1
6334167287_F

tag: cell type


title: Skeletal Muscle Sample 2


title: 26558-2f Liver Tumor


title: Skeletal Muscle Sample 3


title: Neonate_Listeria_2h_subj3

description:
Neonate subject 3
7680504080_B


title: 26558-5m +/-  Liver Tumor


title: Neonate_unstim_2h_subj5

description:
Neonate subject 5
8381661051_I

value: unstimulated


title: Skeletal Muscle Sample 5


title: 26558-5m  +/- Liver Normal

value: normal liver tissue


title: Neonate_unstim_2h_subj4

description:
Neonate subject 4
8381661051_E

value: Neonate


title: Neonate_Listeria_2h_subj2

description:
Neonate subject 2
7677161016_J


title: 543-3m Liver Tumor


title: Adult_Listeria_6h_subj6

description:
Adult subject 6
7656766087_L

source_name: Peripheral blood

value: Adult


title: Skeletal Muscle Sample 4

value: acute, experimental

value: skeletal muscle


title: Adult_Listeria_6h_subj5

description:
Adult subject 5
7656766087_H


title: 543-3m Liver Normal


title: Neonate_unstim_2h_subj3

description:
Neonate subject 3
7680504080_A


title: Adult_Listeria_6h_subj3

description:
Adult subject 3
7677161016_H


title: Neonate_unstim_2h_subj6

description:
Neonate subject 6
8381661062_A


title: Skeletal Muscle Sample 1

value: acute, control


title: Neonate_unstim_2h_subj2

description:
Neonate subject 2
7677161016_I


title: Neonate_unstim_2h_subj1

description:
Neonate subject 1
6334167287_E


title: 5740-3m +/- Liver Normal


title: Adult_Listeria_6h_subj4

description:
Adult subject 4
7656766087_D


title: 12945-4f Liver Tumor


title: Adult_unstim_6h_subj6

description:
Adult subject 6
7656766087_K


title: U3A-STAT1CC-NT-2

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

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

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

description: cell culture, U3A, STAT1CC expressing, untreated, rep n

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

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

source_name: cell culture, U3A, STAT1CC expressing, untreated, rep 2

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

growth_protocol: Cells were grown in standard conditions for U3A cell lines as described previously.

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

treatment_protocol: After stable lines were generated expressing wild-type STAT1 or STAT1CC, cells were grown to confluence, then treated with IFN-beta

tag: transgene

value: Control


title: Adult_Listeria_6h_subj2

description:
Adult subject 2
7677161016_D


title: 5740-3m +/- Liver Tumor


title: Adult_Listeria_6h_subj1

description:
Adult subject 1
6334167287_D


title: 12945-2m Liver Tumor


title: 19849-4m +/- Liver Normal


title: Adult_unstim_6h_subj2

description:
Adult subject 2
7677161016_C


title: 19849-4m +/- Liver Tumor


title: Adult_unstim_6h_subj3

description:
Adult subject 3
7677161016_G


title: Adult_Listeria_2h_subj5

description:
Adult subject 5
7656766087_F


title: Adult_unstim_6h_subj5

description:
Adult subject 5
7656766087_G


title: U3A-STAT1-NT-3

description: cell culture, U3A, STAT1 expressing, untreated, rep n

source_name: cell culture, U3A, STAT1 expressing, untreated, rep 3

value: Wild-type STAT1


title: Adult_Listeria_2h_subj3

description:
Adult subject 3
7677161016_F


title: Adult_unstim_6h_subj4

description:
Adult subject 4
7656766087_C


title: U3A-STAT1CC-IFNb-3

description: cell culture, U3A, STAT1CC expressing, Interferon beta (10U/ml) treated, rep n

source_name: cell culture, U3A, STAT1CC expressing, Interferon beta (10U/ml) treated, rep 3

value: Interferon beta (10U/ml)


title: U3A-STAT1-NT-1

source_name: cell culture, U3A, STAT1 expressing, untreated, rep 1


title: Adult_Listeria_2h_subj2

description:
Adult subject 2
7677161016_B


title: Adult_Listeria_2h_subj4

description:
Adult subject 4
7656766087_B


title: U3A-STAT1-IFNb-2

description: cell culture, U3A, STAT1 expressing, Interferon beta (10U/ml) treated, rep n

source_name: cell culture, U3A, STAT1 expressing, Interferon beta (10U/ml) treated, rep 2


title: 5755-2f Liver Normal

value: Adult liver


title: 5755-2f  Liver Tumor

value: liver tumor tissue


title: Adult_unstim_6h_subj1

description:
Adult subject 1
6334167287_C


title: Adult_Listeria_2h_subj1

description:
Adult subject 1
6334167287_B


title: U3A-STAT1CC-IFNb-1

source_name: cell culture, U3A, STAT1CC expressing, Interferon beta (10U/ml) treated, rep 1


title: 5740-4m Liver Tumor

value: AAV-mediated insertional mutagenesis


title: 17420-1m +/- GFP Liver Normal

value: mixed strain of FVB/NJ, C57BL/6, and 129/Sv


title: Adult_unstim_2h_subj4

description:
Adult subject 4
7656766087_A


title: Adult_unstim_2h_subj6

description:
Adult subject 6
7656766087_I


title: Adult_unstim_2h_subj5

description:
Adult subject 5
7656766087_E


title: U3A-STAT1CC-NT-3

source_name: cell culture, U3A, STAT1CC expressing, untreated, rep 3


title: Adult_unstim_2h_subj3

description:
Adult subject 3
7677161016_E


title: 17420-1m +/- Liver Tumor


title: Adult_Listeria_2h_subj6

description:
Adult subject 6
7656766087_J


title: U3A-S1-NT-2

description: U3A cells stably expressing STAT1, untransfected, rep 2

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

source_name: cell culture, U3A-Stat1 untransfected, rep 2

treatment_protocol: After stable lines were generated overexpressing wild-type or inactive mutant PARP9 and DTX3L, cells were grown to confluence, then treated with IFN-beta


title: Day4_Primed with LM-ΔActA, Irradiated and rescue with live LM replicate 3

hyb_protocol: The hybridization cocktail containing the fragmented and Biotin labeled cRNAs was hybridized to The Affymetrix Human Gene 2.0 ST GeneChip. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

data_processing: Gene expression intensities were calculated using GeneChip® Command Console® Software (AGCC) and Expression Console™ Software.

source_name: spleen

label_protocol: Per RNA labeling, 300 nanograms  of total RNA was used in conjunction with the Affymetrix recommended protocol GeneChip WT Terminal Labeling and Controls Kit (Cat#901525) and Ambion WT Expression Kit (cat#4411973)

growth_protocol: BALB/cByJ and CByB6F1 mice were purchased from Jackson Laboratories.(Bar Harbor, ME)

treatment_protocol: Total body g irradiation was performed using a Gammacell 40 Cs-137 irradiator (MDS Nordion, Mississauga, ON) with a dose rate of 65 cGy/min.  Unirradiated animals were confined in an identical acrylic irradiation chamber for the same amount of time as irradiated animals. Mice were immunized with live of attenuated Listeria monocytogenes LM-ΔActA and 4 weeks later were exposed to a sublethal dose of 600 cGy of γ radiation.  Following irradiation, mice were vaccinated with LM-ΔActA at one time.

value: BALB/cByJ and CByB6F1

tag: protocol


title: U3A-STAT1-NT-2

source_name: cell culture, U3A, STAT1 expressing, untreated, rep 2


title: Adult_unstim_2h_subj2

description:
Adult subject 2
7677161016_A


title: U3A-STAT1-IFNb-3

source_name: cell culture, U3A, STAT1 expressing, Interferon beta (10U/ml) treated, rep 3


title: U3A-S1-NT-1

description: U3A cells stably expressing STAT1, untransfected, rep 1

source_name: cell culture, U3A-Stat1 untransfected, rep 1


title: U3A-S1-MUT_PD-1

description: U3A cells stably expressing STAT1, transfected with inactive mutant PARP9 and DTX3L, rep 1

source_name: cell culture, U3A-Stat1 inactive mutant PARP9 and DTX3L overexpressing, rep 1

value: inactive mutant PARP9 and DTX3L


title: Day4_Primed with LM-ΔActA, Irradiated and rescue with live LM replicate 1


title: Day4_Primed with LM-ΔActA, Irradiated and rescue with live LM replicate 2


title: q024_p_15_M_19

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description:
patient
array: HumanHT-12 V3.0

hyb_protocol: not provided

scan_protocol: Slides were scanned using Illumina BeadStation, and the signal was extracted by using Illumina BeadStudio software.

data_processing:
Raw data were analyzed by using Bioconductor packages in the R statistical environment.  Quality assessment was performed by examining the interarray Pearson correlation and clustering based on the top variant genes was assessed. Contrast analysis of differential expression was performed by using the LIMMA package.  After linear model fitting, a Bayesian estimate of differential expression was calculated.
This study included the use of two different arrays: Illumina HumanHT-12 V3.0 and HumanHT-12 V4.0. The raw and processed data (quantile normalized, log2 transformed data) for each array and the shared probes between the arrays that were analyzed in this study are available on the series level. The final processed data used in the analysis is available in the file "normalized_ageOut.csv" where age was regressed out.

source_name: patient

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

extract_protocol: RNA was extracted from whole blood using the PAXgene extraction kit (Qiagen), then stored at -80C for subsequent analysis, as described below. RNA quantity was assessed with Nanodrop (Nanodrop Technologies) and quality with the Agilent Bioanalyzer (Agilent Technologies).

value: whole blood

tag: diagnosis

value: patient

tag: Sex

value: M

tag: psychoticdisorder

value: no

tag: asd status

value: ASD


title: U3A-STAT1-IFNb-1

source_name: cell culture, U3A, STAT1 expressing, Interferon beta (10U/ml) treated, rep 1


title: U3A-S1-MUT_PD-3

description: U3A cells stably expressing STAT1, transfected with inactive mutant PARP9 and DTX3L, rep 3

source_name: cell culture, U3A-Stat1 inactive mutant PARP9 and DTX3L overexpressing, rep 3


title: U3A-STAT1CC-IFNb-2

source_name: cell culture, U3A, STAT1CC expressing, Interferon beta (10U/ml) treated, rep 2


title: U3A-S1-WT_PD-4

description: U3A cells stably expressing STAT1, transfected with wild-type PARP9 and DTX3L, rep 4

source_name: cell culture, U3A-Stat1 wild-type PARP9 and DTX3L overexpressing, rep 4

value: Wild-type PARP9 and DTX3L


title: U3A-S1-WT_PD-2

description: U3A cells stably expressing STAT1, transfected with wild-type PARP9 and DTX3L, rep 2

source_name: cell culture, U3A-Stat1 wild-type PARP9 and DTX3L overexpressing, rep 2


title: q023_c_12_M_18

description:
control- brother of q_00022
array: HumanHT-12 V3.0

source_name: control- brother of q_00022

tag: tissue

value: healthy control


title: Q0133_c_42_F_70

description:
mother of q_0132
array: HumanHT-12 V4.0

source_name: mother of q_0132

value: F


title: Adult_unstim_2h_subj1

description:
Adult subject 1
6334167287_A

source_name: Peripheral blood

value: Adult

value: monocytes

tag: treatment

value: unstimulated


title: Q0132_p_14_F_70

description:
patient
array: HumanHT-12 V4.0

value: non


title: Q0131_c_48_F_69

description:
mother of q_0130
array: HumanHT-12 V4.0

source_name: mother of q_0130


title: Q0130_p_22_F_69

description:
patient
array: HumanHT-12 V4.0


title: q021_p_10_F_17

description:
patient
array: HumanHT-12 V3.0


title: Q0129_c_49_M_38

description:
adoptive father of q_0059
array: HumanHT-12 V4.0

source_name: adoptive father of q_0059


title: Day4_Primed with LM-ΔActA and Irradiated replicate 2


title: Q0128_c_60_F_38

description:
adoptive mother of q_0059
array: HumanHT-12 V4.0

source_name: adoptive mother of q_0059


title: q020_c_9_M_16

description:
control-brother of q_00019
array: HumanHT-12 V3.0

source_name: control-brother of q_00019


title: Q0127_c_6_M_68

description:
control
array: HumanHT-12 V4.0

source_name: control


title: U3A-S1-WT_PD-3

description: U3A cells stably expressing STAT1, transfected with wild-type PARP9 and DTX3L, rep 3

source_name: cell culture, U3A-Stat1 wild-type PARP9 and DTX3L overexpressing, rep 3


title: U3A-STAT1CC-NT-1

source_name: cell culture, U3A, STAT1CC expressing, untreated, rep 1

value: Control


title: Day4_Primed with LM-ΔActA and Irradiated replicate 1

source_name: spleen


title: Day4_Primed with LM-ΔActA and Irradiated replicate 3


title: U3A-S1-MUT_PD-2

description: U3A cells stably expressing STAT1, transfected with inactive mutant PARP9 and DTX3L, rep 2

source_name: cell culture, U3A-Stat1 inactive mutant PARP9 and DTX3L overexpressing, rep 2


title: Q0126_c_17_M_68

description:
control
array: HumanHT-12 V4.0


title: q019_p_12_M_16

description:
patient
array: HumanHT-12 V3.0

source_name: patient


title: Day4_Primed with LM-ΔActA, rescue with live LM replicate 3


title: Q0125_c_43_F_67

description:
mother of q_0125
array: HumanHT-12 V4.0

source_name: mother of q_0125


title: Q0124_p_14_M_67

description:
patient
array: HumanHT-12 V4.0


title: U3A-S1-NT-3

description: U3A cells stably expressing STAT1, untransfected, rep 3

source_name: cell culture, U3A-Stat1 untransfected, rep 3


title: U3A-S1-WT_PD-1

description: U3A cells stably expressing STAT1, transfected with wild-type PARP9 and DTX3L, rep 1

source_name: cell culture, U3A-Stat1 wild-type PARP9 and DTX3L overexpressing, rep 1


title: q022_p_10_M_18

description:
patient
array: HumanHT-12 V3.0


title: q017_p_6_F_15

description:
patient
array: HumanHT-12 V3.0


title: Q0123_c_48_F_66

description:
mother of q_0122
array: HumanHT-12 V4.0

source_name: mother of q_0122


title: q025_c_40_M_19

description:
father of q_0024
array: HumanHT-12 V3.0

source_name: father of q_0024


title: q016_p_17_M_14

description:
patient
array: HumanHT-12 V3.0


title: q015_p_14_M_13

description:
patient
array: HumanHT-12 V3.0


title: Q0122_p_12_M_66

description:
patient
array: HumanHT-12 V4.0

value: yes


title: Q0121_c_37_F_65

description:
mother of q_0120
array: HumanHT-12 V4.0

source_name: mother of q_0120


title: Day4_Primed with LM-ΔActA, replicate 2

description: Day4_Primed with LM-ΔActA, replicate 2

value: Day4_Primed with LM-ΔActA


title: q011_p_6_M_12

description:
patient
array: HumanHT-12 V3.0


title: Q0120_p_10_F_65

description:
patient
array: HumanHT-12 V4.0


title: q007_p_19_F_1

description:
patient
array: HumanHT-12 V3.0


title: q006_c_39_F_10

description:
mother of q_0005
array: HumanHT-12 V3.0

source_name: mother of q_0005


title: Day4_Primed with LM-ΔActA, rescue with live LM replicate 2

value: BALB/cByJ and CByB6F1


title: Q0119_c_48_F_64

description:
mother of q_0118
array: HumanHT-12 V4.0

source_name: mother of q_0118


title: Day4_Primed with LM-ΔActA, replicate 1

description: Day4_Primed with LM-ΔActA, replicate 1


title: Q0118_p_18_F_64

description:
patient
array: HumanHT-12 V4.0


title: Q0117_c_13_M_63

description:
control
array: HumanHT-12 V4.0


title: Day1_Primed with LM-ΔActA, Irradiated and rescue with live LM replicate 3


title: q014_p_13_M_3

description:
brother of q_0013 and son of 90003
array: HumanHT-12 V3.0

source_name: brother of q_0013 and son of 90003


title: pancreas-wildtype-2

description: mouse pancreas gene expression, baseline, wild-type, C57BL/6J, male.

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

source_name: mouse pancreas obtained at baseline

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

treatment_protocol: Mice were untreated and uninfected.

tag: gender

value: Male

tag: genotype

value: WT


title: Day4_Primed with LM-ΔActA, rescue with live LM replicate 1

tag: strain


title: Day4_Primed with LM-ΔActA, replicate 3

description: Day4_Primed with LM-ΔActA, replicate 3


title: Q0116_c_60_F_62

description:
grandmother of q_0114
array: HumanHT-12 V4.0

source_name: grandmother of q_0114

value: whole blood

tag: age


title: pancreas-Stat1tg-1

description: mouse pancreas gene expression, baseline, Stat1-Transgenic, C57BL/6J, male.


title: pancreas-wildtype-1


title: pancreas-Stat1CCtg-1

description: mouse pancreas gene expression, baseline, Stat1-CC-Transgenic, C57BL/6J, male.


title: pancreas-Stat1tg-2


title: Day1_Primed with LM-ΔActA, Irradiated and rescue with live LM replicate 1


title: Day1_Primed with LM-ΔActA and Irradiated replicate 3


title: pancreas-Stat1tg-3


title: Q0115_c_35_F_62

description:
mother of q_0114
array: HumanHT-12 V4.0

source_name: mother of q_0114


title: Day1_Primed with LM-ΔActA and Irradiated replicate 1


title: q069_p_25_M_5

description:
patient
array: HumanHT-12 V3.0

value: patient

value: M


title: q002_c_42_M_8

description:
father of q_0001
array: HumanHT-12 V3.0

source_name: father of q_0001


title: pancreas-Stat1CCtg-2


title: Day1_Primed with LM-ΔActA and Irradiated replicate 2


title: q068_p_49_M_4

description:
adult patient
array: HumanHT-12 V3.0

source_name: adult patient

value: no


title: Q0114_p_6_F_62

description:
patient
array: HumanHT-12 V4.0


title: q001_p_17_F_8

description:
patient
array: HumanHT-12 V3.0

value: ASD


title: Day1_Primed with LM-ΔActA, Irradiated and rescue with live LM replicate 2

source_name: spleen


title: Day1_Primed with LM-ΔActA, rescue with live LM replicate 3


title: Q0113_c_31_F_61

description:
mother of q_0112
array: HumanHT-12 V4.0

source_name: mother of q_0112

value: healthy control


title: Q0112_p_8_F_61

description:
patient
array: HumanHT-12 V4.0

source_name: patient

value: F


title: pancreas-wildtype-3


title: q065_p_41_F_1

description:
adult patient /mom of q_0007
array: HumanHT-12 V3.0

source_name: adult patient /mom of q_0007


title: Q0111_c_18_M_60

description:
control
array: HumanHT-12 V4.0

source_name: control


title: Q0109_c_21_M_58

description:
control
array: HumanHT-12 V4.0


title: Day1_Primed with LM-ΔActA, rescue with live LM replicate 2


title: q067_p_34_F_3

description:
adult patient /mom of q_0013 and q_0014
array: HumanHT-12 V3.0

source_name: adult patient /mom of q_0013 and q_0014


title: Q0107_c_50_M_57

description:
father of q_0105
array: HumanHT-12 V4.0

source_name: father of q_0105


title: q066_p_61_F_2

description:
adult patient
array: HumanHT-12 V3.0


title: Day1_Primed with LM-ΔActA, rescue with live LM replicate 1


title: Liver_HP-HS-HF

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

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

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.22.0).

organism: Rattus norvegicus

source_name: pool of hepatic RNA of n=5 mice fed the 'high protein - high sucrose - high fat' diet

label_protocol: The Ambion WT Expression kit (Life Technologies, P/N 4411974  ) in conjunction with the Affymetrix GeneChip WT Terminal Labelling kit (Affymetrix, Santa Clara, CA; P/N 900671 ) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. RNA (100 ng) was labelled with the Whole Transcript Sense Target Assay (Affymetrix, Santa Clara, CA).

growth_protocol: Thirty adult male Wistar rats (Harlan, Ganat, France) with initial body weight of 300-350g were housed in individual stainless steel cages in a temperature (23 ± 1 °C) and humidity-(55 ± 3 %) controlled room with an artificial 12:12 h light-dark reverse cycle (light off at 10:00). The rats were adapted to the laboratory conditions and the diet protocol (with normoprotein diet (NP)) for the first 10 days. Rats were accustomed to receiving their food according to a pattern that consisted of a calibrated meal of 87.6 kJ between 09:00 and 10:00, and free access to food between 11:00 and 18:00. This pattern trained the animals to eat a standard meal within one hour, so as to standardize both the amount of energy ingested and the physiological state of animals that were to be studied in a fed state on the day of the experiment.

extract_protocol: Total RNA was isolated from liver samples using TRIzol reagent (Invitrogen, Breda, The Netherlands). After extraction, total RNA was purified using SV total RNA isolation system (Promega, Leiden, the Netherlands). Total purified liver RNA of 5 rats per group was subsequently pooled at a concentration of 1500 ng/rat. Quality of the pooled RNA was assessed on Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips using the Eukaryote Total RNA Nano assay (Agilent Technologies, Amsterdam, the Netherlands). RNA quality was considered as sufficient for array hybridisation if RNA integrity number was ≥ 7.0.

treatment_protocol: After ten days on the NP diet, animals were weight-matched and assigned to one of the six dietary groups with varying amounts of protein (P), carbohydrates (C) and fat (F). Please refer to Table 1 of the manuscript for exact nutrient and energy composition of the diets (note: Table 1 is also attached to this submission). Animals were fed their respective diet for 5 weeks (33 to 37 days), and at the day of dissection they were killed 2hrs after the calibrated morning meal. During the whole experiment rats had free access to water.

value: Wistar

value: male

value: liver


title: Liver_HP-HS

source_name: pool of hepatic RNA of n=5 mice fed the 'high protein - high sucrose - low fat' diet


title: Q0106_c_44_F_57

description:
mother of q_0105
array: HumanHT-12 V4.0

source_name: mother of q_0105


title: pancreas-Stat1CCtg-3


title: Day1_Primed with LM-ΔActA, replicate 3

description: Day1_Primed with LM-ΔActA, replicate 3

value: Day1_Primed with LM-ΔActA


title: Q0108_c_40_F_16

description:
mother of q_0019, q_0020
array: HumanHT-12 V4.0


title: Liver_HP

source_name: pool of hepatic RNA of n=5 mice fed the 'high protein - low fat' diet


title: Liver_NP-HS

source_name: pool of hepatic RNA of n=5 mice fed the 'normal protein - high sucrose - low fat' diet


title: Day1_Primed with LM-ΔActA, replicate 2

description: Day1_Primed with LM-ΔActA, replicate 2


title: Liver_NP

source_name: pool of hepatic RNA of n=5 mice fed the 'normal protein - low fat' diet


title: Liver_NP-HS-HF

source_name: pool of hepatic RNA of n=5 mice fed the 'normal protein - high sucrose - high fat' diet


title: Q0103_c_6_M_10

description:
control, brother of q_0005
array: HumanHT-12 V4.0

source_name: control, brother of q_0005


title: NCI-H716 + miR200ba429 + miR200c141

city: Amsterdam

first: Louis

last: Vermeulen

address: Meibergdreef 9

department: Center for Experimental Molecular Medicine

institute: Academic Medical Center

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: Data were RMA normalized

source_name: colorectal cancer cell line with methylated miR-200 loci

label_protocol: Not provided

extract_protocol: For single- and double-transduced cells, RNA was extracted 7 days after transduction using the NucleoSpin miRNA kit (Macherey-Nagel) and Microarrays of miR-200 overexpressing cell lines were performed using the GeneTitanTM MC system from Affymetrix according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany, on Affymetrix u133 plus 2.0 arrays.

treatment_protocol: Four CCS3 cell lines with high miR-200 promoter methylation (HUTU-80, MDST8, NCI-H716, and SW620) were transduced with lentiviral supernatant and sorted on GFP-positive cells after 48 hours. 24 hours after sorting a fraction of the miR-200ba429 transduced cells was transduced with miR-200c141 lentivirus.

tag: cell line

value: colorectal cancer


title: Control (Veh 24h)

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

description: SAMPLE 1

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina MouseRef-8

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal  Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1

source_name: TA muscles

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: injected with

value: vehicle (control)

value: tibialis anterior (TA) muscle


title: NCI-H716 + miR200c141


title: 3 weeks post-injured [exon-level]

city: Changzhou

first: Ding

last: Ya

state: Jiangsu

address: No. 185 Juqian street

department: Department of Orthopedics

country: China

institute: The Third Affiliated Hospital of Suzhou University

description: T10 spinal cord 3 weeks post-injured

hyb_protocol: GeneChip2 Hybridization, Wash, and Stain Kit (Affymetrix, Inc. US) was used for hybridization

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Affymetrix GCOS Software
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: wild-type, injured spinal cord

label_protocol: GeneChip2 WT Terminal Labeling Kit and Controls Kit (Affymetrix, Inc. US) was used for fragmentation and labeling of this single-stranded DNA

growth_protocol: not applicable

extract_protocol: All samples were snap frozen in liquid N2 and prepared using Trizol. RNA were purified using RNeasy Mini Kit (Qiagen, German), including a DNase digestion treatment. cDNA synthesis and amplification was performed using the GeneChip WT PLUS Reagent Kit (Affymetrix, Inc. US)

treatment_protocol: not applicable

value: ICR

tag: genotype/variation

value: wild-type

value: 4 weeks

value: spinal cord injury

value: 3 weeks post-injured


title: Heart_PCI_rep.4

city: Jena

first: S.

last: Lambeck

address: Erlanger Allee 101

country: Germany

institute: JUH

description: in vivo

hyb_protocol: Hybridization was in agreement with the Whole-Genome Gene Expression Direct Hybridization Assay protocol from Illumina.

scan_protocol: Arrays were readout with the detection system iScan from Illumina.

data_processing: Raw data were obtained using GenomeStudio (v 1.9.0)  and annotation by MouseRef-8_V2_0_R3_11278551_A.bgx.xml. Robust spline normalization (rsn) and detection filtering were performed via lumi package within Bioconductor and R.

source_name: heart muscle tissue, 6h sepsis (PCI)

label_protocol: Amplification and biotinylation of RNA were carried out using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip® (Epicentre).

growth_protocol: Animal experiments were carried out after approval of the local ethics committee.

extract_protocol: RNA was isolated from heart muscle tissue using QIAcubeTM and RNeasy® Mini Kit from Qiagen in accordance to the Purification of Total RNA from Animal Cells Using Spin Technology protocol and the Purification of Total RNA from Animal Tissues protocol, respectively. RNA concentration and purity were determined with the NanoDrop® ND-2000c spectrophotometer and quality control was performed with the automated electrophoresis system ExperionTM (Bio-Rad Laboratories) according to the manufacturer’s specifications using the ExperionTM RNA StdSens Analysis Kit.

treatment_protocol: Referring to a recently published rodent model (Gonnert et al., J Surg Res. 2011), male 20 to 30 weeks old C57BL/6 Jackson mice were subjected to peritoneal contamination and infection (PCI). The animals received an intraperitoneal injection of 5 µl/g BW of a standardised human faeces suspension (4,25 ∙ 107 CFU/g BW; predicted to be lethal). Untreated mice were used as controls.

value: heart muscle


title: Q0102_c_8_F_56

description:
control, sister of q_0101
array: HumanHT-12 V4.0

source_name: control, sister of q_0101

value: whole blood


title: Heart_PCI_rep.3

description: in vivo


title: MDST8 + miR200ba429


title: DHT 24h

description: SAMPLE 2

value: DHT


title: MRC5 NC

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: MRC5 cell

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

tag: transfection


title: Q0101_c_10_F_56

description:
control, brother of q_0102
array: HumanHT-12 V4.0

source_name: control, brother of q_0102

value: healthy control