title: Ambient CO2 fully expanded leaf replicate 1

city: Urbana

first: Robert

middle: John Cody

last: Markelz

address: 1206 W Gregory Dr

department: Plant Biology

institute: University of Illinois

description: gene expression data from mature, youngest most fully expanded leaf 10

hyb_protocol: Labeling was performed by the Keck Center University of Illinois Urbana-Champaign Following manufacturers protocols using the 3' IVT Express Kit User Manual

scan_protocol: Wash and Scanning were performed by the Keck Center University of Illinois Urbana-Champaign Following manufacturers protocols using the Expression Wash, Stain, Scan User Manual for Cartridge Arrays Manual on an Affymetrix model 3000 scanner

data_processing: The data were analyzed using JMP Genomics Version 5.1 (SAS Institute, Inc., Cary NC, USA) using the Basic Expression Workflow Option with the median intensity normalization method option. Probesets not called present in at least 3 biological replicates for each treatment combination were considered insufficiently replicated and were dropped,  leaving 12826 remaining for the analysis.

source_name: Leaf 10 fully expanded

growth_protocol: Arabidopsis thaliana (Col) seeds were soaked in deionized water for 15 min and planted directly on LC1 sunshine mix in 216 cm^2 pots. Planted pots were cold treated in the dark at 4 degrees C for 48 hr prior to being placed into growth chambers with 10/14 day/night cycle with 21/18 degrees C temperature cycle and 300 micromol per meter squared per second photosynthetically active radiation. Plants were kept at 370 ppm CO2 during this period.

extract_protocol: Whole plants were harvested into liquid nitrogen followed by penetration of RNA-Later ICE to allow for leaf primordia to be dissected. 20 individual plants per biological replicate were harvested for the primorida developmental timepoint. Expanding and mature leaves were harvested in full and frozen in liquid nitrogen. All tissue was stored at -80 C, ground frozen and RNA was s isolated using a Spectra Plant RNA Isolation Kit (Sigma) following manufacturers instructions.

treatment_protocol: After 7 days in the growth chambers, plants were randomized between two identical Conviron growth chambers retrofitted for CO2 control. Ambient CO2 was kept at a constant 370 ppm while elevated CO2 was maintained at a constant 750 ppm.

tag: genotype

value: wild-type

tag: cultivar


title: Elevated CO2 fully expanded leaf replicate 3

status: Public on Apr 04 2014

type: RNA

state: IL

country: USA

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: Labeling was performed by the Keck Center University of Illinois Urbana-Champaign Following manufacturers protocols using the 3' IVT Express Kit User Manual


title: Ambient CO2 leaf primordia replicate 4

description: gene expression data from  leaf 10 primordia

source_name: Leaf 10 Primordia


title: Ambient CO2 fully expanded leaf replicate 3


title: Ambient CO2 leaf primordia replicate 3


title: Elevated CO2 leaf primordia replicate 3


title: Elevated CO2 leaf primordia replicate 4


title: Ambient CO2 leaf primordia replicate 2


title: Ambient CO2 leaf primordia replicate 1


title: Ambient CO2 fully expanded leaf replicate 4


title: Elevated CO2 fully expanded leaf replicate 1


title: EC15a

city: Singapore

first: Shugui

last: Wang

address: Biopolis Way, Matrix

country: Singapore

institute: Danone Nutricia research

description: bacteria are from Infant stool

hyb_protocol: Hybridization were done using GEArray S Series Human Immunology Signaling Pathways Gene Array kit. In summary, before pre-hybridization, membranes were pre-wet by adding roughly 5ml of deionized water to the hybridization tube. Warm the GEAhyb Hybridization Solution (in the kit) to 60°C, and then add 2ml of the GEAhyb Hybridization Solution into each tube. The membranes were then pre-hybridized in the oven at 60°C for 24h with continuous agitation at 5-10rpm.  The hybridization step was done according to the manufacture’s instruction. The target hybridization solution was prepared by adding 5µg of biotin labeled cRNA to 1ml of prewarmed GEAhyb Hybridization solution. The solution was then mixed well by pipetting and kept at 60°C till use. The pre-hybridization solution from the hybridization tube was discarded and the Target Hybridization Mix was added into the membrane in the hybridization tube. The membranes were then hybridized overnight at 60°C with continuous agitation (5-10rpm). After hybridization, the Target Hybridization Mix was poured off. The membranes were washed by Wash Solution 1 (2x SSC, 1%SDS) 10min twice at 60°C and Wash Solution 2 (0.1x SSC, 0.5%SDS) 7min twice at 60°C with 20-30 rpm agitation.

scan_protocol: The signals were then detected using Chemiluminenscent detection Kit (Superarray, USA) according to the manufacture’s instruction. Image were acquired by exposing to X-ray film (Koda, USA), the images were then scanned using image scanner (Amersham, UK) and analyzed.

data_processing: The signals were analyzed using the web-based GEArray Expression Analysis Suite (Supperarray, US); Empty spots: positions 399, 398, 400; internal control spots: positions 411, 412, 413, 414, 415, 416

organism: Homo sapiens

source_name: E.faecalis EC15 replicate 1

label_protocol: cDNA was synthesized using AmpoLabeling-LPR Kit. Briefly, Briefly, 1.5µg of total RNA was used for constructing the cDNA. RNA was mixed with 1µl RT primer and appropriate RNase free H2O to get a total volume of 10µl.  The contents were mixed well by gentle pipetting up and down 2 to 3 times followed by a brief centrifugation to collect the mixture at the bottom of the tube. The mixture was then incubated at 70°C for 3min followed by a brief centrifugation. Tubes were placed on ice immediately and kept at 37°C for 10min.  The cDNA Synthesis Master Mix was mixed well and put on ice for use. For each array, transfer 10µl of the cDNA Synthesis Master Mix to the 10µl Annealing Mixture. They were mixed well but gently with a pipetting up and down 2 to 3 times followed by a brief centrifugation to collect the mixture at the bottom of the tube. The mixtures were then continued to be incubated at 37°C for 25min.  After that, they were heated at 85°C for 5min to hydrolyze the RNA and to inactivate the reverse transcriptase. The finished RT Reactions were then held on ice until the next step. For each array, add 30µl of the LPR Cocktail to each RT reaction (20µl) and mixed well but gently with a pipettor. Before denaturing the probes for hybridization, the incorporation efficiency of dUTP with probe was checked according to the manufacture’s instruction (Superarray, USA).  The labeled cDNA probes were then denatured by heating the tube containing the LPR at 94°C for 2min, and quickly chilling on ice. The cDNA probe is now ready for hybridization.

growth_protocol: HCT116 cells were cultured in 24 well plate

extract_protocol: RNA was extracted after a 6h incubation of cell culture with 1 x 107 or 108cfu/ml of bacteria, using the High Pure RNA Isolation Kit (Roche Applied Science, Germany). The wells were washed once with 1ml of ice cold PBS to remove excess bacterial cells, and resuspended in 200μl of PBS. Lysis-binding buffer was added to each well (400μl per well) and residual cells were scrapped off the well bottom before adding the cell lysate to the filter and collection tubes. The tubes were centrifuged at 10,000g for 15sec to remove the buffer while RNA remained bound to the glass fiber fleece on the filter tubes. DNase was added to each tube to digest contaminating DNA for 15min. The RNA was purified from salts, proteins and other cellular impurities using the wash buffer provided in the kit followed by centrifugation before elution from the glass fiber fleece. RNA was then kept at -70°C immediately.

treatment_protocol: Cells were treated with different bacteria

tag: cell line

tag: treatment

value: E.faecalis EC15


title: EC1b

description: bacteria are from Infant stool

source_name: E.faecalis EC1 replicate 2

value: E.faecalis EC1


title: Elevated CO2 fully expanded leaf replicate 2


title: EC1c

description: bacteria are from Infant stool

source_name: E.faecalis EC1 replicate 3


title: Elevated CO2 fully expanded leaf replicate 4


title: Ambient CO2 fully expanded leaf replicate 2


title: C'

description: bacteria are from Infant stool

source_name: Replicate of control

value: control


title: Elevated CO2 leaf primordia replicate 1


title: Elevated CO2 expanding leaf replicate 3

description: gene expression data from expanding leaf 10

source_name: Leaf 10 during rapid expansion


title: Ambient CO2 expanding leaf replicate 3


title: Ambient CO2 expanding leaf replicate 2


title: Elevated CO2 expanding leaf replicate 2


title: Elevated CO2 leaf primordia replicate 2


title: EC1a

description: bacteria are from Infant stool

source_name: E.faecalis EC1 replicate 1


title: C

description: bacteria are from Infant stool

source_name: Control


title: Ambient CO2 expanding leaf replicate 1


title: Elevated CO2 expanding leaf replicate 1


title: Lamina Propria_TM-LP_rep2

status: Public on Apr 03 2014

city: Heidelberg

first: Judith

last: Gras

address: INF 305

country: Germany

institute: University Hospital Heidelberg

hyb_protocol: standard WG-DASL Human HT_12 V4 Assay protocol

scan_protocol: Microarray scanning was done using an Illumina iScan array scanner

data_processing: Data extraction was done for all beads individually, and outliers are removed when the absolute difference to the median is greater than 2.5 times MAD(2.5 Hampel’s method). All remaining bead level data points are than quantile normalized. As test for significance the student’s t-test is used on the bead expression values of the two groups of interest. In the case of significance of expression against background we tested for greater than all negative beads for this sample and in the case of comparing separate groups we tested for inequality of the means of the groups. In both cases Benjamini-Hochberg correction was applied to the complete set of p-values of all 48107 ProbeIDs on the chip. The average expression value is calculated as mean of the measured expressions of beads together with the standard deviation of the beads.

source_name: Lamina Propria at t = 0 h (isolated from colonic TM via LMD)

extract_protocol: LMD followed by RNA isolation with RNeasy Micro Kit (Qiagen)

tag: tissue

value: healthy Colonic Lamina Propria

tag: timepoint

value: 0 h


title: Lamina Propria_LEL-LP_rep1

source_name: Lamina Propria at t = 5 h (isolated from colonic LEL-M via LMD)

label_protocol: standard WG-DASL Human HT_12 V4 Assay protocol

value: EDTA treated

value: 5 h


title: human MSC2

city: Taipei

first: Jir-You

address: Department of Orthopaedic & Traumatology, Taipei Veterans General Hospital, 201, Sec 2, Shih-Pai Road, Taipei 112, Taiwan

department: Department of Orthopaedics & Traumatology

country: Taiwan

institute: Taipei Veterans General Hospital

description: primary cell from osteosarcoma patient 2 disease-free bone marrow

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: human MSC2

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up

tag: cell type

value: primary cell from disease-free bone marrow

tag: disease state

value: osteosarcoma


title: MSC OeMyc

description: parental MSC overexpression c-Myc

source_name: MSC OeMyc

value: parental MSC overexpression c-Myc

value: healthy


title: human MSC1

description: primary cell from osteosarcoma patient 1 disease-free bone marrow

source_name: human MSC1


title: Lamina Propria_TM-LP_rep3


title: human OS3

description: primary cell from osteosarcoma patient 3 tumor part

source_name: human OS3

value: primary cell from tumor


title: Lamina Propria_LEL-LP_rep4


title: MSC SiRb

description: parental MSC silence Rb

source_name: MSC SiRb

value: parental MSC silence Rb


title: MSC SiRb-OeMyc1

description: parental MSC silence Rb and overexpress c-Myc-1

source_name: MSC SiRb-OeMyc1


title: MSC SiRb-OeMyc2

description: parental MSC silence Rb and overexpress c-Myc-2

source_name: MSC SiRb-OeMyc2


title: human OS1

description: primary cell from osteosarcoma patient 1 tumor part

source_name: human OS1


title: Lamina Propria_LEL-LP_rep3


title: Lamina Propria_TM-LP_rep4


title: parental MSC2

description: primary cell from healthy human bone marrow

source_name: parental MSC2


title: human OS2

description: primary cell from osteosarcoma patient 2 tumor part

source_name: human OS2


title: human MSC3

description: primary cell from osteosarcoma patient 3 disease-free bone marrow

source_name: human MSC3


title: Lamina Propria_LEL-LP_rep2


title: parental MSC1

source_name: parental MSC1

value: primary cell from healthy human bone marrow


title: TS753D_NF1-shRNA #2-3

city: Boston

first: Markus

last: Riester

state: MA

address: 3 Blackfan Circle

department: Biostatistics & Computational Biology

institute: Dana-Farber Cancer Institute

description:
replicate 3
hGBM_sphere study

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.10.0). It was vst transformed and quantile normalized.

source_name: Human GBM sphere line (TS753D) expressing the NF1-shRNA (#2)-3

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: batch

tag: vector constructs

value: pLKO.1-NF1shRNA (#2), SKI-RSI-192342, MSKCC


title: TS753D_NF1-shRNA #2-2

description:
replicate 2
hGBM_sphere study

source_name: Human GBM sphere line (TS753D) expressing the NF1-shRNA (#2)-2


title: Lamina Propria_TM-LP_rep1


title: TS753D_Control shRNA-3

description:
replicate 3
hGBM_sphere study

source_name: Human GBM sphere line (TS753D) expressing the empty control vector-3

value: pLKO.1-empty vector, SKI-RSI-249999, MSKCC


title: TS753D_Control shRNA-2

description:
replicate 2
hGBM_sphere study

source_name: Human GBM sphere line (TS753D) expressing the empty control vector-2


title: TS753D_Control shRNA-4

description:
replicate 4
hGBM_sphere study

source_name: Human GBM sphere line (TS753D) expressing the empty control vector-4


title: TS753D_NF1-shRNA #5-4

description:
replicate 4
hGBM_sphere study

source_name: Human GBM sphere line (TS753D) expressing the NF1-shRNA (#5)-4

value: pLKO.1-NF1shRNA (#5), SKI-RSI-192345, MSKCC


title: TS753D_NF1-shRNA #2-4

description:
replicate 4
hGBM_sphere study

source_name: Human GBM sphere line (TS753D) expressing the NF1-shRNA (#2)-4


title: TS753D_Control shRNA-1

description:
replicate 1
hGBM_sphere study

source_name: Human GBM sphere line (TS753D) expressing the empty control vector-1


title: TS753D_NF1-shRNA #2-1

description:
replicate 1
hGBM_sphere study

source_name: Human GBM sphere line (TS753D) expressing the NF1-shRNA (#2)-1


title: TS753D_NF1-shRNA #5-3

description:
replicate 3
hGBM_sphere study

source_name: Human GBM sphere line (TS753D) expressing the NF1-shRNA (#5)-3


title: TS753D_NF1-shRNA #5-2

description:
replicate 2
hGBM_sphere study

source_name: Human GBM sphere line (TS753D) expressing the NF1-shRNA (#5)-2


title: TS753D_NF1-shRNA #5-1

description:
replicate 1
hGBM_sphere study

source_name: Human GBM sphere line (TS753D) expressing the NF1-shRNA (#5)-1


title: TS667_NF1-shRNA (#2)_Rapamycin-1

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#2), Rapamycin treatment-1


title: TS667_NF1-shRNA (#2)_DMSO-1

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#2), DMSO treatment-1


title: TS543_Control shRNA-2

description:
replicate 2
hGBM_sphere study

source_name: Human GBM sphere line (TS543) expressing the empty control vector-2


title: TS543_Control shRNA-3

description:
replicate 3
hGBM_sphere study

source_name: Human GBM sphere line (TS543) expressing the empty control vector-3


title: TS667_NF1-shRNA (#5)_Rapamycin-3

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#5), Rapamycin treatment-3


title: TS667_NF1-shRNA (#5)_Rapamycin-2

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#5), Rapamycin treatment-2


title: TS667_NF1-shRNA (#5)_Rapamycin-1

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#5), Rapamycin treatment-1


title: TS667_NF1-shRNA (#2)_DMSO-3

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#2), DMSO treatment-3


title: TS667_NF1-shRNA (#5)_DMSO-2

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#5), DMSO treatment-2


title: TS543_NF1-shRNA (#5)_Rapamycin-2

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#5), Rapamycin treatment-2


title: TS543_NF1-shRNA (#5)_Rapamycin-3

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#5), Rapamycin treatment-3


title: TS667_NF1-shRNA (#2)_Rapamycin-2

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#2), Rapamycin treatment-2


title: L024 vs S036.L024_repl4

city: Hamburg

first: Stefan

last: Scholten

state: Hamburg

address: Ohnhorststrasse 18

department: Biocenter Klein Flottbek

institute: University of Hamburg

description: L024 vs S036.L024

hyb_protocol: The hybridization and post-hybridization followed the protocol of the Maize Oligo Array Project (http://www.maizearray.org/).

scan_protocol: The slides were scanned using an AppliedPrecision ArrayWorx Scanner (Applied Precision Inc., USA).

data_processing:
Data normalization was performed using the LIMMA package (version 2.9) from Bioconductor (Gentleman et al., Genome Biology 2004, 5:R80). For assessing differential expression, the normexp background correction method with the parameter offset=50 was applied to each array and resulted in strictly positive adjusted intensities. The adjusted signal intensities were normalized using a two-step normalization: weighted print-tip group loess normalization of log-ratios (within-array normalization) followed by quantile normalization of average log-intensities of two channels (between-array normalization). Between-array normalization for the two inbreds-hybrid comparisons P033.F047 and F047.P048 was seperately performed from the residual comparisons.  A series of positive control probes were given double weight to assist the normalization process.
Provided supplementary file contains mean normalized log2 expression value of each gene-related oligo of each genotype from an inbreds-hybrid comparison. The values consists of normalized replicate values from two arrays of the total three arrays of each inbreds-hybrid comparison. For example "1_F012 (F012.P024)" describes the normalized expression of the genotype F012 derived from the comparison of the hybrid F012.P024 and its inbred parents. These data represent the absolute values used in the associated manuscript.

organism: Zea mays

source_name: whole 7 day old seedling

label_protocol: Aminoallyl-RNA was labeled with either Cy5 or Cy3 following the "Amino Allyl MessageAmp II aRNA Amplification Kit" protocol (Applied Biosystems/Ambion, Austin, USA).

growth_protocol: Inbred maize plants were grown in climate chamber under controlled conditions (25 °C 16 h day, 21 °C 8 h night, 70 % air humidity) for seven days.

extract_protocol: Total RNA was extracted with an extraction buffer (200 mM NaCl, 50mM Tris pH 9, 5 mM EDTA pH 8, 1  % SDS), phenol/chloroform and selective LiCl (4M) precipitation.

value: Flint

value: interpool-hybrid


title: TS667_NF1-shRNA (#5)_DMSO-1

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#5), DMSO treatment-1


title: TS543_NF1-shRNA (#2)_Rapamycin-1

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#2), Rapamycin treatment-1


title: L024 vs S036.L024_repl2

description: L024 vs S036.L024


title: L024 vs S036.L024_repl3

description: L024 vs S036.L024


title: Fibroblasts, mild phenotype, biological rep 3

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

description:
FB1637IIpiastra
Gene expression data from cultured fibroblasts from monozygotic twin.

hyb_protocol: Hybridization was performed according to Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Affymetrix scanner.

data_processing: The data were normalized and background corrected using the GCRMA function in R/Bioconductor.

label: Biotin

source_name: fibroblasts, mild phenotype

label_protocol: cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Primary fibroblast cultures were established from biopsies. Cells were routinely subcultured and used for experiments at passage 6 to 8.

extract_protocol: Total RNA was extracted by cultured fibroblasts with TRIzol (Life Technologies).

value: fibroblast

tag: disease status

value: recessive dystrophic epidermolysis bullosa (RDEB)

tag: phenotype

value: mild


title: TS543_NF1-shRNA (#2)_DMSO-3

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#2), DMSO treatment-3


title: TS543_NF1-shRNA (#5)_DMSO-3

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#5), DMSO treatment-3


title: Fibroblasts, mild phenotype, biological rep 2

description:
FB1637Ipiastra
Gene expression data from cultured fibroblasts from monozygotic twin.


title: TS543_NF1-shRNA (#2)_Rapamycin-3

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#2), Rapamycin treatment-3


title: TS543_NF1-shRNA (#5)_DMSO-1

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#5), DMSO treatment-1


title: Fibroblasts, severe phenotype, biological rep 3

description:
FB1636IIpiastra
Gene expression data from cultured fibroblasts from monozygotic twin.

source_name: fibroblasts, severe phenotype

value: severe


title: L024 vs S036.L024_repl1

description: L024 vs S036.L024


title: TS543_NF1-shRNA (#5)_Rapamycin-1

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#5), Rapamycin treatment-1


title: S036 vs S036.L024_repl4

description: S036 vs S036.L024

value: Dent


title: Fibroblasts, severe phenotype, biological rep 2

description:
FB1636Ipiastra
Gene expression data from cultured fibroblasts from monozygotic twin.


title: TS667_NF1-shRNA (#2)_DMSO-2

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#2), DMSO treatment-2


title: TS543_NF1-shRNA (#2)_Rapamycin-2

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#2), Rapamycin treatment-2


title: S036 vs S036.L024_repl3

description: S036 vs S036.L024


title: TS667_NF1-shRNA (#5)_DMSO-3

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#5), DMSO treatment-3


title: S036 vs S036.L024_repl2

description: S036 vs S036.L024


title: TS543_Control shRNA-1

description:
replicate 1
hGBM_sphere study

source_name: Human GBM sphere line (TS543) expressing the empty control vector-1


title: TS667_NF1-shRNA (#2)_Rapamycin-3

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS667) expressing the NF1-shRNA (#2), Rapamycin treatment-3


title: S036 vs S036.L024_repl1

description: S036 vs S036.L024


title: TS543_NF1-shRNA (#2)_DMSO-1

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#2), DMSO treatment-1


title: S036 vs L024_repl4

description: S036 vs L024


title: TS543_NF1-shRNA (#2)_DMSO-2

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#2), DMSO treatment-2


title: TS543_NF1-shRNA (#5)_DMSO-2

description: hGBM_rapamycin study

source_name: Human GBM sphere line (TS543) expressing the NF1-shRNA (#5), DMSO treatment-2


title: S036 vs L024_repl2

description: S036 vs L024

source_name: whole 7 day old seedling


title: L024 vs S028.L024_repl3

description: L024 vs S028.L024


title: S036 vs L024_repl1

description: S036 vs L024


title: L024 vs S028.L024_repl4

description: L024 vs S028.L024


title: L024 vs S028.L024_repl1

description: L024 vs S028.L024


title: L024 vs S028.L024_repl2

description: L024 vs S028.L024


title: S028 vs S028.L024_repl4

description: S028 vs S028.L024


title: Fibroblasts, mild phenotype, biological rep 1, technical rep 2

description:
F37b
Gene expression data from cultured fibroblasts from monozygotic twin.


title: S028 vs S028.L024_repl3

description: S028 vs S028.L024


title: S028 vs S028.L024_repl2

description: S028 vs S028.L024


title: T8, phosphate limitation

city: Stuttgart

first: Tom

last: Schuhmacher

address: Allmandring 31

department: Institute of Biochemical Engineering

institute: University of Stuttgart

description: Gene expression under phosphate limitation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip E. coli 2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data was analysed using Genedata analyst 7.0, data extraction was achieved through RMA (Irizarry, Hobbs et al. 2003).

organism: Escherichia coli

source_name: fermentation sample, 28 h

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

growth_protocol: Fed-Batch process applying phosphate limitation through constant phosphate feeding. All other elements were in excess, pH 6,9, 33 °C, 0,5 bar

extract_protocol: Total RNA was extracted using the Rneasy mini kit (Qiagen) according to the manufacturers instructions

treatment_protocol: Samples were taken into 4 volumes RNAprotect solution (Qiagen), aliquots with an RNA content of 10 µg were taken, centrifuged for 5 min at 7500 g, cell pellet stored at -70°C for maximum 4 weeks

tag: strain

tag: fermentation time


title: T9, fermentation end

source_name: fermentation sample, 32 h


title: S028 vs S028.L024_repl1

description: S028 vs S028.L024


title: T6, phosphate limitation

source_name: fermentation sample, 22 h


title: T7, phosphate limitation

source_name: fermentation sample, 25 h


title: S028 vs L024_repl4

description: S028 vs L024


title: S028 vs L024_repl3

description: S028 vs L024


title: T3, phosphate limitation

source_name: fermentation sample, 8 h

value: 8 h


title: T4, phosphate limitation

source_name: fermentation sample, 11 h


title: Fibroblasts, mild phenotype, biological rep 1, technical rep 1

description:
F37
Gene expression data from cultured fibroblasts from monozygotic twin.

source_name: fibroblasts, mild phenotype


title: S028 vs L024_repl2

description: S028 vs L024


title: Fibroblasts, severe phenotype, biological rep 1, technical rep 2

description:
F36b
Gene expression data from cultured fibroblasts from monozygotic twin.

source_name: fibroblasts, severe phenotype


title: S028 vs L024_repl1

description: S028 vs L024


title: T1, phosphate limitation

source_name: fermentation sample, 4 h

value: 4 h


title: Fibroblasts, severe phenotype, biological rep 1, technical rep 1

description:
F36
Gene expression data from cultured fibroblasts from monozygotic twin.


title: F012 vs S028.F012_repl4

description: F012 vs S028.F012


title: T2, phosphate limitation

source_name: fermentation sample, 6 h

value: 6 h


title: T0, phosphate excess

description: Gene expression under phosphate excess

source_name: fermentation sample, 2,5 h


title: T5, phosphate limitation

source_name: fermentation sample, 17 h


title: F012 vs S028.F012_repl2

description: F012 vs S028.F012


title: F012 vs S028.F012_repl3

description: F012 vs S028.F012


title: S028 vs S028.F012_repl1

description: S028 vs S028.F012


title: S028 vs F012_repl4

description: S028 vs F012


title: S028 vs S028.F012_repl4

description: S028 vs S028.F012


title: S028 vs F012_repl2

description: S028 vs F012


title: PWS_iPS_1

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description: Gene expression data from PWS-iPSC-1

hyb_protocol: Affymetrix protocol, 11 µg cRNA

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console (RMA)

source_name: Induced pluripotent stem cells dervied from PWS individual 1 fibroblasts

label_protocol: 200 ng total RNA, Affymetrix protocol

extract_protocol: Total RNA was extracted using PerfectPure RNA Cultured Cell Kit (5 PRIME)

tag: material

value: Cell line

tag: gender

value: Female

value: Undifferentiated induced pluripotent stem cells


title: PWS_iPS_3

description: Gene expression data from PWS-iPSC-3

source_name: Induced pluripotent stem cells dervied from PWS individual 3 fibroblasts

value: Male


title: F047 vs P048.F047_repl4

description: F047 vs P048.F047


title: PWS_iPS_2

description: Gene expression data from PWS-iPSC-2

source_name: Induced pluripotent stem cells dervied from PWS individual 2 fibroblasts


title: F047 vs P048.F047_repl3

description: F047 vs P048.F047


title: F012 vs S028.F012_repl1

description: F012 vs S028.F012


title: F047 vs P048.F047_repl2

description: F047 vs P048.F047


title: PWS_fibroblast_2

description: Gene expression data from PWS-Fib-2

source_name: PWS individual 2 fibroblasts

value: Fibroblasts


title: Cre + dCDK

city: La Jolla

first: Steven

last: Dowdy

state: CA

address: 9500 Gilman Drive #0686

department: CMM

institute: UCSD

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

organism: Mus musculus

source_name: murine embryonic fibroblast

growth_protocol: Murine embryonic fibroblasts grown under standard conditions: DMEM + 10% FBS, 5% CO2, 37 deg.

extract_protocol: Total RNA was isolated with RNeasy Plus and QIAshredder (Qiagen)  in accordance with the prescribed protocol provided with the kit.

value: embryonic fibroblast

tag: tat-cre treatment

value: TAT-Cre (2 1h treatments, 3h apart)

tag: retroviral infection

value: dCDK RB retrovirus (2 1h infections, 3h apart)

tag: genotype/variation

value: exogenous phospho-mutant RB, expressed at time of RB deletion


title: Cre + WT

value: wt RB retrovirus (2 1h infections, 3h apart)

value: exogenous wildtype RB, expressed at time of RB deletion


title: Cre

value: media alone (2 1h treatments, 3h apart)

value: Rb deletion


title: S028 vs F012_repl3

description: S028 vs F012

source_name: whole 7 day old seedling

tag: genotype

tag: cultivar

value: Flint

value: Dent


title: S028 vs F012_repl1

description: S028 vs F012


title: F047 vs P048.F047_repl1

description: F047 vs P048.F047

value: interpool-hybrid


title: P048 vs P048.F047_repl4

description: P048 vs P048.F047


title: No Cre

value: solution lacking TAT-Cre (2 1h treatments, 3h apart)

value: control (unaltered)


title: RCAS-shNf1_2

description:
replicate 2
Murine sphere study

source_name: N/tv-a neuroshere expressing the RCAS-shNf1

value: Nestin (N)/tv-a

tag: rcas vector


title: RCAS-shp53_2

description:
replicate 2
Murine sphere study

source_name: N/tv-a neuroshere expressing the RCAS-shp53


title: RCAS-shGL2_3

description:
replicate 3
Murine sphere study

source_name: N/tv-a neuroshere expressing the RCAS-shGL2


title: RCAS-shNf1_1

description:
replicate 1
Murine sphere study


title: RCAS-shNf1+shp53_3

description:
replicate 3
Murine sphere study

source_name: N/tv-a neuroshere expressing the RCAS-shNf1/shp53


title: RCAS-shNf1+shp53_2

description:
replicate 2
Murine sphere study


title: P048 vs P048.F047_repl3

description: P048 vs P048.F047


title: RCAS-shp53_3

description:
replicate 3
Murine sphere study


title: P048 vs P048.F047_repl1

description: P048 vs P048.F047


title: P048 vs P048.F047_repl2

description: P048 vs P048.F047


title: S036 vs L024_repl3

description: S036 vs L024


title: RCAS-shp53_1

description:
replicate 1
Murine sphere study


title: P048 vs F047_repl4

description: P048 vs F047


title: P048 vs F047_repl3

description: P048 vs F047


title: RCAS-shNf1+shp53_1

description:
replicate 1
Murine sphere study


title: RCAS-shNf1_3

description:
replicate 3
Murine sphere study


title: P048 vs F047_repl2

description: P048 vs F047


title: P048 vs F047_repl1

description: P048 vs F047


title: P033 vs P033.F047_repl4

description: P033 vs P033.F047


title: P033 vs P033.F047_repl3

description: P033 vs P033.F047


title: F047 vs P033.F047_repl4

description: F047 vs P033.F047


title: F047 vs P033.F047_repl3

description: F047 vs P033.F047


title: F047 vs P033.F047_repl2

description: F047 vs P033.F047


title: F047 vs P033.F047_repl1

description: F047 vs P033.F047


title: P033 vs P033.F047_repl1

description: P033 vs P033.F047


title: 1989_N/tv-a; PDGF-A/shp53/shNf1

description: Murine gliomas study

source_name: Murine brain tumor, N/tv-a wt, RCAS-PDGF-A/shp53/shNf1 injection

value: Nestin (N)/tv-a wt

value: PDGF-A-myc/His + shp53 (mR696) + shNf1 (GR249)

tag: tumor latency (days)

tag: tumor grade

value: GBM

tag: sample id


title: 1878_N/tv-a; PDGF-A/shp53/shNf1

description: Murine gliomas study


title: 2032_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-A

description: Murine gliomas study

source_name: Murine brain tumor, N/tva; Ink4a-Arf-/-; Ptenfl/fl, RCAS-PDGF-A injection

value: N/tva; Ink4a-Arf-/-; Ptenfl/fl

value: PDGF-A-myc/His


title: RCAS-shGL2_2

description:
replicate 2
Murine sphere study

tag: batch


title: RCAS-shGL2_1

description:
replicate 1
Murine sphere study


title: 1875_N/tv-a; PDGF-A/shp53/shNf1

description: Murine gliomas study


title: F047 vs P033_repl3

description: F047 vs P033


title: 1844_N/tv-a; PDGF-A/shp53/shNf1

description: Murine gliomas study


title: F047 vs P033_repl4

description: F047 vs P033


title: F047 vs P033_repl2

description: F047 vs P033


title: 1886_N/tv-a; PDGF-A/shp53

description: Murine gliomas study

source_name: Murine brain tumor, N/tv-a wt, RCAS-PDGF-A/shp53 injection

value: PDGF-A-myc/His + shp53 (mR696)


title: F047 vs P033_repl1

description: F047 vs P033


title: 1895_N/tv-a; PDGF-A/shp53

description: Murine gliomas study


title: S028 vs S028.F039_repl4

description: S028 vs S028.F039


title: 1861_G/tv-a; PDGF-A/shp53/shNf1

description: Murine gliomas study

source_name: Murine brain tumor, G/tv-a wt, RCAS-PDGF-A/shp53/shNf1 injection

value: GFAP (G)/tv-a wt


title: 1890_G/tv-a; PDGF-A/shp53

description: Murine gliomas study

source_name: Murine brain tumor, G/tv-a wt, RCAS-PDGF-A/shp53 injection


title: 1926_N/tv-a; PDGF-A/shp53

description: Murine gliomas study


title: 1851_G/tv-a; PDGF-A/shp53/shNf1

description: Murine gliomas study


title: 1837_G/tv-a; PDGF-A/shp53/shNf1

description: Murine gliomas study


title: 1881_N/tv-a; PDGF-A/shp53

description: Murine gliomas study


title: 1840_G/tv-a; PDGF-A/shp53/shNf1

description: Murine gliomas study


title: 1841_N/tv-a; PDGF-A/shp53

description: Murine gliomas study


title: S028 vs S028.F039_repl2

description: S028 vs S028.F039


title: S028 vs S028.F039_repl1

description: S028 vs S028.F039


title: S028 vs S028.F039_repl3

description: S028 vs S028.F039


title: F039 vs S028.F039_repl4

description: F039 vs S028.F039


title: F039 vs S028.F039_repl3

description: F039 vs S028.F039


title: F039 vs S028.F039_repl2

description: F039 vs S028.F039


title: 1882_G/tv-a; PDGF-A/shp53

description: Murine gliomas study


title: 1809_G/tv-a; PDGF-A/shp53

description: Murine gliomas study


title: F039 vs S028.F039_repl1

description: F039 vs S028.F039


title: 1883_G/tv-a; PDGF-A/shp53

description: Murine gliomas study

value: ND


title: 1807_G/tv-a; PDGF-A/shp53

description: Murine gliomas study


title: F039 vs S028_repl3

description: F039 vs S028


title: F039 vs S028_repl2

description: F039 vs S028


title: F039 vs S028_repl1

description: F039 vs S028


title: P024 vs P024.F039_repl3

description: P024 vs P024.F039


title: P024 vs P024.F039_repl4

description: P024 vs P024.F039


title: F039 vs S028_repl4

description: F039 vs S028


title: P024 vs P024.F039_repl2

description: P024 vs P024.F039


title: 1924_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-A/shNf1

description: Murine gliomas study

source_name: Murine brain tumor, N/tva; Ink4a-Arf-/-; Ptenfl/fl, RCAS-PDGF-A/shNf1 injection

value: PDGF-A-myc/His + shNf1 (GR249)


title: 1913_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-A/shNf1

description: Murine gliomas study


title: P024 vs P024.F039_repl1

description: P024 vs P024.F039


title: F039 vs P024.F039_repl4

description: F039 vs P024.F039


title: input DNA

type: SRA

city: Research Triangle Park

first: Sylvia

middle: C

last: Hewitt

state: NC

address: 111 Alexander Dr

department: RDBL

institute: NIEHS

library_source: genomic

data_processing:
Sequences (36 nucleotide reads) were aligned to the mouse genome (National Center for Biotechnology Information Build 37.1/mm9) using Eland (Illumina pipeline) software.
Duplicate mapped reads were removed with MarkDuplicates.jar from the Picard suite (v1.62).
ER alpha peak calls were made with Partek Genomics Suite (v 6.11.1101; Partek, Inc, St Louis, MO) using default parameters.
Called peaks were filtered to exclude peaks with Mann-Whitney P-value > 0.01.
Mapped reads were extended at their 3' end to a length equal to the estimated average fragment size for that library and then converted to aggregate coverage (bedGraph format) with BEDtools genomeCoverageBed.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph file per sample showing aggregate coverage of mapped extended reads; generated by BEDtools genomeCoverageBed.
Supplementary_files_format_and_content: Called ER alpha peaks (idnetified via Partek Genomic Suite) in BED format.

molecule: genomic DNA

source_name: uterus

growth_protocol: mice were maintained on NIH-31 chow, standard light/dark cycle, 1-5 mice per cage

extract_protocol:
Uteri were submersed in PBS + 1% formaldehyde, cut into small (~1 mm3) pieces with a razor blade and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearor (Biospec Products, Bartlesville, OK) and finally spun down and washed 2x in PBS. Chromatin was isolated from the sample by adding 5-10 ml lysis buffer containing PIPES, Igepal, PMSF and Protease Inhibitor Cocktail, followed by disruption with a Dounce homogenizer. Samples were pelleted by centrifugation and resuspended in buffer containing Na deoxycholate, SDS, and Triton X-100. Lysates were sonicated using a Misonix Sonicator 3000 (Misonix, Farmingdale, NY) equipped with a microtip in order to shear the DNA to an average length of 300-500 bp. Lysates were cleared by centrifugation and the chromatin suspensions were transferred to new tubes and stored at -80 C. To prepare Input DNA (genomic DNA), two aliquots of 10-25 µl each (approximately 1/50 of each chromatin preparation) were removed and treated with RNase for 1-2 h at 37 C, proteinase K for 3 h at 37 C, and 65 C heat for at least 6 h to overnight for de-crosslinking. DNAs were purified by phenol-chloroform extraction and ethanol precipitated. Pellets were resuspended in 1/5 TE. Resulting DNAs were quantified on a Nanodrop spectrophotometer (Thermo Scientific, Wilmington, DE). Extrapolation to the original chromatin volume allowed determination of the yield for each chromatin preparation, as measured by the DNA content.  Prior to use in ChIP, protein A agarose beads (Invitrogen Technologies, Carlsbad, CA) were preblocked using blocking proteins and nucleic acids for 3 h. For each ChIP reaction, an aliquot of chromatin (20-30 µg) was precleared with 30 µl preblocked protein A agarose beads for 1-2 h. ChIP reactions were set up using precleared chromatin and antibody to ERα (sc-542, Santa Cruz Inc, Santa Cruz CA) or PolII phospho Ser5 (ab5095, Abcam, Cambridge, MA) in a buffer containing Na deoxycholate and incubated overnight at 4 C. Preblocked protein A agarose beads were added and incubation at 4 C was continued for another 3 h. Agarose beads containing the immune complexes were washed two times each with a series of buffers consisting of the deoxycholate sonication buffer, high salt buffer, LiCl buffer, and TE buffer. An SDS-containing buffer was added to elute the immune complexes from the beads, and the eluates were subjected to RNase treatment at 37 C for 20 min and proteinase K treatment at 37 C for 3 h. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNAs were purified by phenol/chloroform extraction and ethanol precipitation. Quality of ERα ChIP enrichment was assayed by qPCR using primers against candidate EREs in the Igf1 and Stat5a promoters (9). Quality of PolII ChIP enrichment was assayed by qPCR using primers against region in Intron 1 of the housekeeping genes Actin B and  Gapdh. Input DNA was queried at the same sites in parallel.
ChIP DNA was amplified by following the Illumina ChIP-Seq DNA Sample Prep Kit (Illumina, Inc.  San Diego, California)  protocol. In brief, DNA ends were polished and 5’-phosphorylated using T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. After addition of 3’-A to the ends using Klenow fragment (3’-5’ exo minus), Illumina genomic adapters were ligated and the sample was size fractionated (200-250 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles, Phusion polymerase, New England Bioloabs, Ipswich, MA), the resulting DNA libraries were quantified and tested by qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions. DNA libraries were sequenced on a Genome Analyzer II (Illumina).

treatment_protocol: mice were ovariectomized and injected intraperitoneally 10-14 days later with saline vehicle or estradiol (250 ng/mouse). Uterine tissue was collected one hour later

tag: antibody

tag: background mouse strain


title: 1929_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-A/shNf1

description: Murine gliomas study


title: 1909_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-A/shNf1

description: Murine gliomas study


title: 1888_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-A

description: Murine gliomas study


title: 1919_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-A/shNf1

description: Murine gliomas study


title: F039 vs P024.F039_repl3

description: F039 vs P024.F039


title: 1937_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-A

description: Murine gliomas study


title: 1855_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-A

description: Murine gliomas study


title: 1817_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-A

description: Murine gliomas study


title: 1485_N/tva; Ink4a-Arf-/-; Ptenfl/fl; normal brain

description: Murine gliomas study

source_name: Normal brain tissue (frontal lobe), N/tva; Ink4a-Arf-/-; Ptenfl/fl, no injection

value: 53 days old


title: F039 vs P024.F039_repl1

description: F039 vs P024.F039


title: 1805_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-A

description: Murine gliomas study


title: 1486_N/tva; Ink4a-Arf-/-; Ptenfl/fl; normal brain

description: Murine gliomas study


title: 1475_N/tva; Ink4a-Arf-/-; Ptenfl/fl; shNf1/Cre

description: Murine gliomas study

source_name: Murine brain tumor, N/tva; Ink4a-Arf-/-; Ptenfl/fl, RCAS-shNf1/Cre injection

value: shNf1 (GR249) + cre


title: yeast-mcd1-Apr2011-3

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The Affymetrix Yeast Genome 2.0 array contains probes designed for both S. pombe and S. cerevisiae. Data from the arrays was filtered to exclude probes annotated to S. pombe, and retain those annotated to S. cerevisiae genes. Array intensities were processed using the RMA algorithm in the affy library (version affy_1.36.1) from bioconductor in R version 2.15.2.

organism: Saccharomyces cerevisiae

source_name: yeast mcd1 mutant, Rec8 from Mcd1 promoter

label_protocol: Biotinylated cRNA was prepared from 300 ng Total RNA using MessageAmp III aRNA Kit from Ambion.

growth_protocol: Cultures were innoculated from fresh overnights and grown at 30C in YPD+CSM to an OD as indicated.

extract_protocol: Total RNA was extracted using the hot acid phenol method.

treatment_protocol: Cells growing in exponential phase in YPD+CSM were pelleted by centrifugation.

value: mcd1 mutant, Rec8 from Mcd1 promoter

tag: replicate


title: F039 vs P024.F039_repl2

description: F039 vs P024.F039

value: Flint


title: F039 vs P024_repl4

description: F039 vs P024

value: Dent


title: 1484_N/tva; Ink4a-Arf-/-; Ptenfl/fl; normal brain

description: Murine gliomas study

tag: strain


title: 1446_N/tv-a; shNf1/shp53

description: Murine gliomas study

source_name: Murine brain tumor, N/tv-a wt, RCAS-shNf1/shp53 injection


title: F039 vs P024_repl3

description: F039 vs P024


title: 1218_N/tv-a; shNf1/shp53

description: Murine gliomas study


title: 1323_N/tv-a; normal brain

description: Murine gliomas study

source_name: Normal brain tissue (frontal lobe), N/tv-a wt, no injection

value: 176 days old


title: 1293_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-B

description: Murine gliomas study

source_name: Murine brain tumor, N/tva; Ink4a-Arf-/-; Ptenfl/fl, RCAS-PDGF-B injection

value: PDGF-B-HA


title: 1294_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-B

description: Murine gliomas study


title: 1288_N/tva; Ink4a-Arf-/-; Ptenfl/fl; shNf1/Cre

description: Murine gliomas study


title: 1447_N/tva; Ink4a-Arf-/-; Ptenfl/fl; shNf1/Cre

description: Murine gliomas study


title: 1322_N/tva; Ink4a-Arf-/-; Ptenfl/fl; normal brain

description: Murine gliomas study

value: 116 days old


title: 1182_new_N/tv-a; shNf1/shp53

description: Murine gliomas study

value: Nestin (N)/tv-a wt


title: 1877_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-A

description: Murine gliomas study


title: F039 vs P024_repl1

description: F039 vs P024

source_name: whole 7 day old seedling


title: yeast-mcd1-Apr2011-1


title: F039 vs P024_repl2

description: F039 vs P024


title: 1324_N/tv-a; normal brain

description: Murine gliomas study

value: 134 days old


title: F039 vs F012.F039_repl4

description: F039 vs F012.F039

value: intrapool-hybrid


title: yeast-mcd1-Apr2011-2


title: yeast-mcd1_fob1-pRec8-Apr2011-3

source_name: yeast mcd1 fob1 double mutant, Rec8 from Mcd1 promoter


title: F039 vs F012.F039_repl2

description: F039 vs F012.F039


title: F039 vs F012.F039_repl3

description: F039 vs F012.F039


title: yeast-mcd1_fob1-pRec8-Apr2011-2

value: mcd1 fob1 double mutant, Rec8 from Mcd1 promoter


title: F039 vs F012.F039_repl1

description: F039 vs F012.F039


title: yeast-mcd1_fob1-pRec8-Apr2011-1


title: F012 vs F012.F039_repl4

description: F012 vs F012.F039


title: yeast-wt-Jun2011-3

source_name: yeast wt control

value: wild type control


title: yeast-wt-Jun2011-2


title: 1120_200_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-B

description: Murine gliomas study

value: N/tva; Ink4a-Arf-/-; Ptenfl/fl

value: GBM


title: yeast-wt-Jun2011-1


title: F012 vs F012.F039_repl3

description: F012 vs F012.F039


title: 1213_N/tv-a; normal brain

description: Murine gliomas study

value: 343 days old


title: F012 vs F012.F039_repl2

description: F012 vs F012.F039


title: yeast-rad61_eco1-Apr2011-2

source_name: yeast eco1 rad61 double mutant

value: eco1 rad61 double mutant


title: yeast-rad61_eco1-Apr2011-3


title: 1212_N/tv-a; normal brain

description: Murine gliomas study


title: 1122_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-B

description: Murine gliomas study


title: 1121_N/tva; Ink4a-Arf-/-; Ptenfl/fl; PDGF-B

description: Murine gliomas study


title: 1197_N/tv-a; shNf1/shp53

description: Murine gliomas study


title: F012 vs F012.F039_repl1

description: F012 vs F012.F039


title: Pten Null Cancer Cells, Biological Replicate 3

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description: Biological replicate 3 of 3. Prostate cancer epithelial cells

hyb_protocol: Experimental and reference probes were combined and hybridized to custom Agilent 4x44K  whole mouse genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer's suggested protocol

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2565BA (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software was used was used for background subtraction and LOWESS normalization.  Spots of poor quality (p-value < 0.05) were removed from further analysis

source_name: MGS

label_protocol: A total of 825 ng of amplified amino-allyl aRNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl aRNA was labeled with Cy5) following Agilent suggested protocols.

extract_protocol: All samples were laser-capture microdissected (~5000 cells per sample).  Total RNA was isolated using the Arcturus PicoPure RNA Isolation kit (Molecular Devices, Sunnyvale, CA) and DNAse-treated using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA).  Total RNA was then amplified two rounds using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), incorporating amino-allyl UTP into second round aRNA according to the manufacturer's specification.

tag: tissue

value: reference pool of normal adult tissues (10% prostate and 30% each testis, liver, and kidney)

value: male

value: Swiss-Webster

source_name: Pten null cancer cells

value: tumor prostate tissue at anterior lobe

value: mixed background

value: Pb-Cre+;PtenL/L

tag: age

value: 28-30 weeks


title: yeast-rad61_eco1-Apr2011-1


title: yeast-rad61-Apr2011-3

source_name: yeast rad61 mutant

value: rad61 mutant


title: Pten Null Cancer Cells, Biological Replicate 2

description: Biological replicate 2 of 3. Prostate cancer epithelial cells

tag: gender


title: Pten Null Cancer Cells, Biological Replicate 1

description: Biological replicate 1 of 3. Prostate cancer epithelial cells


title: F012 vs F039_repl4

description: F012 vs F039

value: Flint


title: 1162_N/tv-a; shNf1/shp53

description: Murine gliomas study

value: Nestin (N)/tv-a wt


title: Benign Prostatic Epithelial Cells, Biological Replicate 3

description: Biological replicate 3 of 3.  Control benign prostate epithelial cells

source_name: Benign epithelial cells

value: benign prostate tissue at anterior lobe

value: Pb-Cre-;PtenL/L


title: yeast-rad61-Apr2011-2


title: 1129_N/tva; Ink4a-Arf-/-; Ptenfl/fl; shNf1/Cre

description: Murine gliomas study

value: shNf1 (GR249) + cre


title: Benign Prostatic Epithelial Cells, Biological Replicate 2

description: Biological replicate 2 of 3.  Control benign prostate epithelial cells


title: Benign Prostatic Epithelial Cells, Biological Replicate 1

description: Biological replicate 1 of 3.  Control benign prostate epithelial cells


title: 1760_G/tv-a; normal brain

description: Murine gliomas study

source_name: Normal brain tissue (frontal lobe), G/tv-a wt, no injection

value: GFAP (G)/tv-a wt

value: 194 days old


title: F012 vs F039_repl3

description: F012 vs F039


title: yeast-rad61-Apr2011-1


title: 1118_N/tv-a; shNf1/shp53

description: Murine gliomas study

value: GBM


title: 1761_G/tv-a; normal brain

description: Murine gliomas study


title: F012 vs F039_repl2

description: F012 vs F039


title: 1759_G/tv-a; normal brain

description: Murine gliomas study


title: 1183_N/tv-a; shNf1/shp53

description: Murine gliomas study


title: F012 vs F039_repl1

description: F012 vs F039


title: yeast-fob1-Jun2011-3

source_name: yeast fob1 mutant

value: fob1 mutant


title: P024 vs P024.F012_repl2

description: P024 vs P024.F012

value: Dent

value: interpool-hybrid


title: P024 vs P024.F012_repl3

description: P024 vs P024.F012


title: P024 vs P024.F012_repl1

description: P024 vs P024.F012


title: yeast-fob1-Jun2011-2


title: P024 vs P024.F012_repl4

description: P024 vs P024.F012


title: yeast-fob1-Apr2011-3


title: PTEN-CaP2 Cell Line Replicate 3

description: Biological replicate 1 of 3.  Prostatic epthelial cells; homozygous for Pten deletion

growth_protocol: Cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS; Omega Scientific), 25 μg/mL bovine pituitary extract, 5 μg/mL bovine insulin, and 6 ng/mL recombinant human epidermal growth factor (rhEGFR; Sigma-Aldrich)

extract_protocol: Total RNA was isolated using the Arcturus PicoPure RNA Isolation kit (Molecular Devices, Sunnyvale, CA) and DNAse-treated using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA), and was then amplified two rounds using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), incorporating amino-allyl UTP into second round aRNA according to the manufacturer's specification.

value: reference pool of normal adult tissues (10% prostate and 30% each testis, liver, and kidney)

value: male

value: Swiss-Webster

source_name: PTEN-CaP2 cells

tag: cell line

value: Pten null


title: yeast-fob1-Apr2011-2


title: yeast-fob1-Jun2011-1


title: PTEN-CaP2 Cell Line Replicate 2

description: Biological replicate 2 of 3.  Prostatic epthelial cells; homozygous for Pten deletion


title: yeast-fob1-Apr2011-1


title: 1757_G/tv-a; normal brain

description: Murine gliomas study

value: 150 days old


title: PTEN-P2 Cell Line Replicate 3

description: Biological replicate 3 of 3.  Prostatic epthelial cells; heterozygous for Pten deletion

source_name: PTEN-P2 cells

value: Pb-Cre+;PtenL/W


title: PTEN-P2 Cell Line Replicate 2

description: Biological replicate 2 of 3.  Prostatic epthelial cells; heterozygous for Pten deletion


title: F012 vs P024.F012_repl3

description: F012 vs P024.F012

value: Flint


title: PTEN-CaP2 Cell Line Replicate 1


title: PTEN-CaP8 Cell Line Replicate 3

source_name: PTEN-CaP8 cells


title: yeast-eco1_fob1-Apr2011-3

source_name: yeast eco1 fob1 double mutant

value: eco1 fob1 double mutant


title: 1758_G/tv-a; normal brain

description: Murine gliomas study


title: 1752_G/tv-a; shNf1/shp53

description: Murine gliomas study

source_name: Murine brain tumor, G/tv-a wt, RCAS-shNf1/shp53 injection


title: yeast-eco1_fob1-Apr2011-2


title: PTEN-P2 Cell Line Replicate 1

description: Biological replicate 1 of 3.  Prostatic epthelial cells; heterozygous for Pten deletion


title: 1747_G/tv-a; shNf1/shp53

description: Murine gliomas study


title: 1745_G/tv-a; shNf1/shp53

description: Murine gliomas study


title: PTEN-CaP8 Cell Line Replicate 1


title: F012 vs P024.F012_repl1

description: F012 vs P024.F012


title: 1734_G/tv-a; shNf1/shp53

description: Murine gliomas study


title: 1733_G/tv-a; shNf1/shp53

description: Murine gliomas study


title: 1732_G/tv-a; shNf1/shp53

description: Murine gliomas study


title: 1743_G/tv-a; shNf1/shp53

description: Murine gliomas study


title: F012 vs P024.F012_repl4

description: F012 vs P024.F012


title: F012 vs P024_repl3

description: F012 vs P024


title: yeast-eco1-Jun2011-3

source_name: yeast eco1 mutant

value: eco1 mutant


title: yeast-eco1-Jun2011-1


title: yeast-eco1-Jun2011-2


title: yeast-eco1_fob1-Apr2011-1


title: F012 vs P024_repl4

description: F012 vs P024


title: F012 vs P024_repl1

description: F012 vs P024


title: PTEN-P8 Cell Line Replicate 2

description: Biological replicate 2 of 3.  Prostatic epthelial cells;heterozygous for Pten deletion

source_name: PTEN-P8 cells


title: F012 vs P024_repl2

description: F012 vs P024

source_name: whole 7 day old seedling


title: PTEN-CaP8 Cell Line Replicate 2


title: PTEN-P8 Cell Line Replicate 1

description: Biological replicate 1 of 3.  Prostatic epthelial cells;heterozygous for Pten deletion


title: 1598_N/tva; Ink4a-Arf-/-; Ptenfl/fl; shNf1/Cre

description: Murine gliomas study

source_name: Murine brain tumor, N/tva; Ink4a-Arf-/-; Ptenfl/fl, RCAS-shNf1/Cre injection

value: N/tva; Ink4a-Arf-/-; Ptenfl/fl


title: PTEN-P8 Cell Line Replicate 3

description: Biological replicate 3 of 3.  Prostatic epthelial cells;heterozygous for Pten deletion


title: Benign Prostate Epithelial Cell Replicate 3

description: Biological replicate 3 of 3.  Control WT prostatic epithelial cells microdissected from benign prostate

source_name: Benign prostate epithelial cells

tag: cell type

value: Benign prostate epithelial cells

value: Pb-Cre-;PtenL/L


title: Benign Prostate Epithelial Cell Replicate 1

description: Biological replicate 1 of 3.  Control WT prostatic epithelial cells microdissected from benign prostate


title: CCL-2 with Coriandrum sativum

city: Piracicaba

first: Irlan

middle: de Almeida

last: Freires

state: Sao Paulo

address: 901 Limeira Ave.

department: Physiological Sciences

country: Brazil

institute: University of Campinas

description: replicate 1

hyb_protocol: Standard Illumina scanning protocol

source_name: Hela Cells

label_protocol: Standard Illumina hybridization protocol

growth_protocol: After being treated with the essentia oil or vehicle, Hela cells were grown for 18 h at 5 % CO2 as recommended by the manufacturer.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Hela cells were treated with the essential oil at inhibitory concentration (30%) - 359.76 ug/ml

tag: treatment

value: Essential oil - Coriandrum sativum


title: CCL-2 with vehicle control

description: replicate 1

value: vehicle - control 24h


title: 1603_N/tva; Ink4a-Arf-/-; Ptenfl/fl; shNf1/Cre

description: Murine gliomas study

value: shNf1 (GR249) + cre


title: 1748_N/tv-a; shNf1/shp53

description: Murine gliomas study

source_name: Murine brain tumor, N/tv-a wt, RCAS-shNf1/shp53 injection

value: Nestin (N)/tv-a wt


title: 1746_N/tv-a; shNf1/shp53

description: Murine gliomas study


title: 1742_N/tv-a; shNf1/shp53

description: Murine gliomas study


title: 1744_N/tv-a; shNf1/shp53

description: Murine gliomas study


title: Benign Prostate Epithelial Cell Replicate 2

description: Biological replicate 2 of 3.  Control WT prostatic epithelial cells microdissected from benign prostate

source_name: MGS

tag: genotype


title: IM013_VN1203_10^3pfu_d1_3

status: Public on Apr 02 2014

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description: Replicate 3.

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K whole mouse genome array (Design ID 014868).

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

source_name: lung, VN1203 10^3 pfu infection, day 1

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

extract_protocol: All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2-fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer's recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Specific lobes of the lung from each animal were harvested and briefly rinse tissue in cold (4ºC) PBS. Following the RNALater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNALater. After a 4ºC incubation for overnight, samples were stored at -80ºC further processing. Lung tissue was removed from RNALater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) Trizol and stored at -80°C until RNA isolation.

tag: strain/background

value: lung

value: VN1203 10^3 pfu infection

tag: timepoint

value: day 1


title: IM013_VN1203_10^4pfu_d7_4

description: Replicate 4.

source_name: lung, VN1203 10^4 pfu infection, day 7

value: VN1203 10^4 pfu infection

value: day 7


title: IM013_VN1203_10^3pfu_d2_4

description: Replicate 4.

source_name: lung, VN1203 10^3 pfu infection, day 2

value: day 2


title: IM013_mock_d7_2

description: Replicate 2.

source_name: lung, mock infection, day 7

value: mock infection


title: IM013_VN1203_10^4pfu_d7_3

description: Replicate 3.


title: IM013_VN1203_10^4pfu_d2_4

description: Replicate 4.

source_name: lung, VN1203 10^4 pfu infection, day 2


title: IM013_VN1203_10^4pfu_d2_1

description: Replicate 1.


title: IM013_VN1203_10^3pfu_d4_1

description: Replicate 1.

source_name: lung, VN1203 10^3 pfu infection, day 4

value: day 4


title: IM013_VN1203_10^4pfu_d7_2

description: Replicate 2.


title: IM013_mock_d1_3

description: Replicate 3.

source_name: lung, mock infection, day 1


title: IM013_VN1203_10^4pfu_d2_3

description: Replicate 3.


title: IM013_mock_d2_2

description: Replicate 2.

source_name: lung, mock infection, day 2


title: IM013_VN1203_10^3pfu_d7_2

description: Replicate 2.

source_name: lung, VN1203 10^3 pfu infection, day 7


title: IM013_VN1203_10^4pfu_d1_2

description: Replicate 2.

source_name: lung, VN1203 10^4 pfu infection, day 1


title: IM013_VN1203_10^3pfu_d1_2

description: Replicate 2.


title: IM013_VN1203_10^3pfu_d1_1

description: Replicate 1.


title: IM013_mock_d7_3

description: Replicate 3.


title: IM013_VN1203_10^4pfu_d4_2

description: Replicate 2.

source_name: lung, VN1203 10^4 pfu infection, day 4


title: IM013_VN1203_10^4pfu_d4_3

description: Replicate 3.


title: IM013_VN1203_10^4pfu_d7_1

description: Replicate 1.


title: IM013_VN1203_10^3pfu_d2_1

description: Replicate 1.


title: IM013_mock_d1_1

description: Replicate 1.


title: IM013_VN1203_10^4pfu_d4_4

description: Replicate 4.


title: IM013_VN1203_10^4pfu_d1_1

description: Replicate 1.


title: IM013_VN1203_10^4pfu_d1_4

description: Replicate 4.


title: IM013_VN1203_10^3pfu_d4_3

description: Replicate 3.


title: IM013_VN1203_10^3pfu_d7_3

description: Replicate 3.


title: F012 vs P024.F012_repl2

description: F012 vs P024.F012

source_name: whole 7 day old seedling

tag: cultivar

value: interpool-hybrid

value: Flint


title: IM013_mock_d4_1

description: Replicate 1.

source_name: lung, mock infection, day 4


title: IM013_VN1203_10^3pfu_d1_4

description: Replicate 4.


title: IM013_VN1203_10^3pfu_d4_2

description: Replicate 2.


title: IM013_VN1203_10^4pfu_d1_3

description: Replicate 3.


title: IM013_mock_d2_1

description: Replicate 1.


title: IM013_VN1203_10^3pfu_d2_2

description: Replicate 2.


title: IM013_VN1203_10^3pfu_d2_3

description: Replicate 3.


title: IM013_VN1203_10^4pfu_d2_2

description: Replicate 2.


title: IM013_mock_d4_2

description: Replicate 2.


title: IM013_VN1203_10^3pfu_d7_1

description: Replicate 1.


title: IM013_VN1203_10^3pfu_d4_4

description: Replicate 4.


title: IM013_mock_d4_3

description: Replicate 3.


title: IM013_mock_d1_2

description: Replicate 2.


title: IM013_VN1203_10^4pfu_d4_1

description: Replicate 1.


title: IM013_mock_d7_1

description: Replicate 1.


title: IM015_RIPK3_CA04_d2_1

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K mouse array.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Lung tissue from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNALater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNALater. After a 4ºC incubation overnight, samples were stored at -80ºC until processing. Lung tissue was removed from RNALater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) Trizol and stored at -80°C until RNA isolation.

value: Lung

tag: mouse strain

value: RIPK3 knock-out

tag: infection


title: IM015_RIPK3_CA04_d2_2


title: IM015_B6_CA04_d4_1


title: IM015_RIPK3_CA04_d4_2


title: IM015_B6_Mock_d4_1

value: Mock


title: IM015_B6_Mock_d2_3


title: IM015_B6_CA04_d4_2


title: IM015_B6_CA04_d2_2


title: IM015_RIPK3_CA04_d4_3


title: IM015_RIPK3_Mock_d4_2


title: IM013_VN1203_10^3pfu_d7_4

description: Replicate 4.


title: IM015_RIPK3_Mock_d4_3


title: IM015_B6_CA04_d4_3


title: IM015_RIPK3_Mock_d2_1


title: IM015_RIPK3_CA04_d4_1


title: IM015_B6_Mock_d2_1


title: IM015_B6_CA04_d2_1


title: IM015_RIPK3_Mock_d2_2


title: IM015_RIPK3_Mock_d4_1


title: Hic2 FL/FL biological replicate 2

city: liverpool

first: Iain

middle: M

last: Dykes

state: Select...

address: James Parson Bl, Byrom Street,

department: Pharmacy & Biomolecular science

country: United Kingdom

institute: Liverpool John Moores University

description: Pool of 4-6 heart samples

hyb_protocol: Mouse Exon 1.0 ST whole transcript array genechip (Affymetrix).

scan_protocol: Affymetrix GeneChip Microarray System at UCL Genomics Institute of Child Health

data_processing: CHP data generated using  Expression Console (affymetrix). RMA algorithm.  Gene core profiles.

source_name: E13.5 Heart

label_protocol: WT Expression kit (Ambion); genechip terminal labelling and hydrolyzing kit (Affymetrix, Santa Clara USA)

extract_protocol: RNA Mini kit (Qiagen)

tag: genotype/variation

value: Hic2 FL/FL


title: Hic2 FL/FL biological replicate 3

description: Pool of 4-6 heart samples


title: IM015_B6_Mock_d2_2


title: Mesp1 Cre/+; Hic2 FL/FL biological replicate 2

description: Pool of 4-6 heart samples

value: Mesp1 Cre/+; Hic2 FL/FL


title: Hic2 FL/FL biological replicate 1

description: Pool of 4-6 heart samples


title: IM015_B6_Mock_d4_2


title: Mesp1 Cre/+; Hic2 FL/FL biological replicate 3

description: Pool of 4-6 heart samples


title: Mesp1 Cre/+; Hic2 FL/FL biological replicate 1

description: Pool of 4-6 heart samples


title: KL12 genomic DNA from Keloid skin tissue

type: genomic

city: Detroit

first: Ana

last: deCarvalho

state: MI

address: 2799 West Grand Blvd.

department: Department of Neurosurgery

institute: Henry Ford Hospital

description: Skin tissue biosy

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

source_name: Keloid skin tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from keloid samples using Qiagen DNeasy Kit according to standard instructions

value: Anonymous

tag: sample type

value: Keloid skin tissue

tag: disease state

value: Keloid


title: KL2 genomic DNA from Normal skin tissue

description: Skin tissue biosy

source_name: Fresh skin tissue

value: Fresh skin tissue

value: normal


title: KL1 genomic DNA from Normal skin tissue

description: Skin tissue biosy


title: KL4 genomic DNA from Normal skin tissue

description: Skin tissue biosy


title: KL8 genomic DNA from Keloid skin tissue

description: Skin tissue biosy


title: UC Sample 234

first: Dennis

address: 30 Medical Drive

institute: Singapore Institute for Clinical Sciences

data_processing: Background subtraction was performed in GenomeStudio then data was exported.  Probes were filtered for detection p-value <0.05 and NBEADS>3 in R.  Data was then loaded into Arraystudio version 6 (Omicsoft). All technical replicates were combined after sample QC. Data were normalised amongst samples using quantile normalization and subjected to Combat to removed batch effect.

label: Cy3 and Cy5

source_name: Umbilical cord

label_protocol: Standard Illumina Infinium HD assay protocol

extract_protocol: A weighed amount of pulverized umbilical cord tissue was lysed and homogenised via Hyaluronidase solution treatment, addition of TNES lysis buffer and Proteinase K.

value: Female

tag: ethnicity

value: Malay

tag: batch


title: UC Sample 233

extract_protocol: A weighed amount of pulverized umbilical cord tissue was lysed and homogenised via Hyaluronidase solution treatment, additionof TNES lysis buffer and Proteinase K.

value: Male

value: Chinese


title: KL9 genomic DNA from Keloid skin tissue

description: Skin tissue biosy


title: KL3 genomic DNA from Normal skin tissue

description: Skin tissue biosy


title: KL5 genomic DNA from Normal skin tissue

description: Skin tissue biosy


title: KL11 genomic DNA from Keloid skin tissue

description: Skin tissue biosy


title: UC Sample 227


title: UC Sample 220


title: UC Sample 235


title: KL6 genomic DNA from Normal skin tissue

description: Skin tissue biosy


title: UC Sample 230


title: UC Sample 225


title: UC Sample 228

value: Indian


title: UC Sample 229


title: UC Sample 237


title: KL10 genomic DNA from Keloid skin tissue

description: Skin tissue biosy


title: UC Sample 221


title: UC Sample 236


title: UC Sample 223


title: UC Sample 232


title: UC Sample 231


title: KL7 genomic DNA from Keloid skin tissue

description: Skin tissue biosy


title: UC Sample 222


title: UC Sample 224


title: Sample 21_742265

city: Changsha

first: zhiping

last: tan

address: 139 Renmin Road

country: China

institute: the Second Xiangya Hospiatl

description: Peripheral blood from congenital heart disease patient of the Second Xiangya Hospital

hyb_protocol: Standard Illumina procedures

scan_protocol: Beadstation Scanner

data_processing: GenomeStudio V2011 and Illumina cnvPartition (V2.3.4); The processed data file linked to each sample records contains the following data columns; GC Score, Theta, R, B Allele Freq, Log R Ratio

label: Cy3, Cy5

source_name: Peripheral blood from PA patient

label_protocol: Standard Illumina procedures

extract_protocol: Genomic DNA was prepared from peripheral blood using a DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA)

tag: subject group

value: pulmonary atresia (PA)

tag: tissue

value: Peripheral blood


title: UC Sample 226

city: Singapore

tag: gender


title: Sample 20_877494


title: UC Sample 219


title: Sample 19_795265


title: UC Sample 218


title: Sample 18_Family2TwinB

source_name: Peripheral blood from ToF/PA

value: ToF/PA (tetralogy of Fallot with pulmonary atresia)


title: Sample 17_Family2TwinA


title: Sample 15_791019


title: Sample 14_882624


title: Sample 13_894147


title: Sample 16_827979

source_name: Peripheral blood from PA patient (intellectual disability)

value: PA, intellectual disability


title: Sample 11_765647


title: Sample 10_875001


title: UC Sample 216


title: UC Sample 217


title: UC Sample 214


title: UC Sample 208


title: Sample 9_706346


title: UC Sample 206


title: Sample 8_894020


title: UC Sample 202


title: UC Sample 213


title: UC Sample 203


title: UC Sample 201


title: UC Sample 205


title: UC Sample 196


title: Sample 6_817646


title: UC Sample 207


title: Sample 7_881678


title: UC Sample 212


title: UC Sample 197


title: UC Sample 194


title: Sample 5_Family1Mother

source_name: Peripheral blood from control

value: Normal control, mother of patient 2 and3


title: UC Sample 209


title: UC Sample 198


title: UC Sample 195


title: UC Sample 199


title: UC Sample 210


title: Sample 4_Family1Father

value: Normal control, Father of patient 2 and 3


title: UC Sample 211


title: Sample 2_Family1 TwinA


title: UC Sample 192


title: UC Sample 200


title: Sample 1_869677


title: Sample 3_Family1TwinB


title: UC Sample 204


title: UC Sample 215


title: UC Sample 191


title: UC Sample 193


title: UC Sample 189


title: UC Sample 190


title: Sample 12_807411


title: UC Sample 184


title: UC Sample 185


title: UC Sample 188


title: UC Sample 182


title: UC Sample 180


title: UC Sample 181


title: UC Sample 183


title: UC Sample 179


title: UC Sample 171


title: UC Sample 167


title: UC Sample 170


title: UC Sample 166


title: UC Sample 169


title: UC Sample 172


title: UC Sample 168


title: UC Sample 173


title: UC Sample 177


title: UC Sample 175


title: UC Sample 176


title: UC Sample 163


title: UC Sample 174


title: UC Sample 165


title: UC Sample 162


title: UC Sample 178


title: UC Sample 164


title: UC Sample 161


title: UC Sample 186


title: UC Sample 158


title: UC Sample 187


title: UC Sample 157


title: UC Sample 159


title: UC Sample 236

hyb_protocol: Standard Illumina protocol; standard hybridization for Illumina is 48C for 16-24 hours

scan_protocol: Standard Illumina protocol on the Illumina iScan

data_processing: Standard Illumina protocol for Infinium Human Genotyping beadchips Beadchip quantificatin and processing in GenomeStudio v2011.1

label: C-Bio and A-DNP

label_protocol: Standard Illumina protocol using the Infinium OmniExpressExome DNA Analysis Kit v 1.2

extract_protocol: A weighed amount of pulverized umbilical cord tissue was lysed and homogenised via Hyaluronidase solution treatment,  addition of TNES lysis buffer and Proteinase K.


title: UC Sample 237


title: UC Sample 234


title: UC Sample 160


title: UC Sample 233


title: UC Sample 151


title: UC Sample 156


title: UC Sample 149


title: UC Sample 155


title: UC Sample 232


title: UC Sample 231


title: UC Sample 235


title: UC Sample 150


title: UC Sample 148


title: UC Sample 153


title: UC Sample 152


title: UC Sample 147


title: UC Sample 227


title: UC Sample 230


title: UC Sample 228


title: UC Sample 146


title: UC Sample 229


title: UC Sample 225


title: UC Sample 154


title: UC Sample 143


title: UC Sample 223


title: UC Sample 224


title: UC Sample 222


title: UC Sample 226


title: UC Sample 145


title: UC Sample 141


title: UC Sample 142


title: UC Sample 138


title: UC Sample 221


title: UC Sample 220


title: UC Sample 140


title: UC Sample 219


title: UC Sample 218


title: UC Sample 137


title: UC Sample 134


title: UC Sample 215


title: UC Sample 139


title: UC Sample 217


title: UC Sample 214


title: UC Sample 132


title: UC Sample 135


title: UC Sample 136


title: UC Sample 144


title: UC Sample 131


title: UC Sample 130


title: UC Sample 129


title: UC Sample 211


title: UC Sample 126


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title: UC Sample 124


title: UC Sample 128


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title: UC Sample 213


title: UC Sample 127


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title: UC Sample 118


title: UC Sample 116


title: UC Sample 196


title: UC Sample 194


title: UC Sample 115


title: UC Sample 195


title: UC Sample 117


title: UC Sample 114


title: UC Sample 119


title: UC Sample 111


title: UC Sample 108


title: UC Sample 193


title: UC Sample 112


title: UC Sample 190


title: UC Sample 110


title: UC Sample 189


title: UC Sample 186


title: UC Sample 107


title: UC Sample 188


title: UC Sample 192


title: UC Sample 109


title: UC Sample 106


title: UC Sample 184


title: UC Sample 183


title: UC Sample 185


title: UC Sample 105


title: UC Sample 102


title: UC Sample 113


title: UC Sample 181


title: UC Sample 100


title: UC Sample 99


title: UC Sample 180


title: UC Sample 97


title: UC Sample 191


title: UC Sample 182


title: UC Sample 98


title: UC Sample 178


title: UC Sample 187


title: UC Sample 101


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title: UC Sample 175


title: UC Sample 177


title: UC Sample 96


title: UC Sample 179


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title: UC Sample 94


title: UC Sample 173


title: UC Sample 93


title: UC Sample 104


title: UC Sample 172


title: UC Sample 174


title: UC Sample 170


title: UC Sample 103


title: UC Sample 168


title: UC Sample 92


title: UC Sample 89


title: UC Sample 88


title: UC Sample 90


title: UC Sample 169


title: UC Sample 167


title: UC Sample 165


title: UC Sample 87


title: UC Sample 83


title: UC Sample 85


title: UC Sample 81


title: UC Sample 166


title: UC Sample 84


title: UC Sample 82


title: UC Sample 86


title: UC Sample 91


title: UC Sample 159


title: UC Sample 163


title: UC Sample 158


title: UC Sample 161


title: UC Sample 160


title: UC Sample 80


title: UC Sample 79


title: UC Sample 157


title: UC Sample 162


title: UC Sample 78


title: UC Sample 77


title: UC Sample 171


title: UC Sample 76


title: UC Sample 164


title: UC Sample 156


title: UC Sample 154


title: UC Sample 155


title: UC Sample 153


title: UC Sample 71


title: UC Sample 152


title: UC Sample 74


title: UC Sample 69


title: UC Sample 68


title: UC Sample 70


title: NG OF KO 3 MICE

city: Dallas

first: Chen

last: Liu

address: 5223 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: ko replicate 3

data_processing: The data were normalised using quantile normalisation with Partek Genomic Suite V6.5

source_name: PPARγ fl/fl

extract_protocol: Nodose ganglia were cryosectioned (25 µm) using a cryostat and thaw-mounted onto silane-coated PEN membrane glass slides (Applied Biosystems, Foster City, CA). Slides were lightly fixed in 75% ethanol immediately prior to thionin staining.  Sections were then dehydrated in a series of graded ethanol baths followed by 5 minutes in xylenes.  The Arcturus Veritas Microdissection System (Applied Biosystems) was used to isolate the neuron-enriched samples from the surrounding fibers and glial cells.  RNA was extracted using a PicoPure RNA Isolation Kit (Applied Biosystems) with an on-column DNAse I treatment to remove genomic contamination (Qiagen, Valencia, CA). RNA quality was determined using the Experion Automated Electrophoresis system (Bio-Rad, Hercules, CA).

treatment_protocol: No treatment

tag: background strain

value: Phox2B::Cre; PPARγ fl/fl_NG


title: UC Sample 73

last: Wang


title: UC Sample 148


title: UC Sample 145


title: UC Sample 67


title: UC Sample 151


title: UC Sample 147


title: UC Sample 149


title: UC Sample 66


title: UC Sample 63


title: UC Sample 65


title: UC Sample 62


title: UC Sample 150


title: NG OF KO 2 MICE

description: ko replicate 2


title: UC Sample 146


title: UC Sample 143


title: UC Sample 142


title: UC Sample 141


title: UC Sample 72


title: UC Sample 75


title: UC Sample 64


title: UC Sample 61


title: UC Sample 138


title: UC Sample 140


title: NG OF KO 1 MICE

description: ko replicate 1


title: NG OF CONTROL 3 MICE

description: control replicate 3

source_name: PPARγ fl/+

value: Phox2B::Cre; PPARγ fl/+_NG


title: UC Sample 139


title: NG OF CONTROL 2 MICE

description: control replicate 2


title: UC Sample 144


title: UC Sample 137


title: Hpx KO Untreated 3

city: Cambridge

first: Jason

middle: H

last: Yang

address: 415 Main St, Rm 2017

department: Biological Engineering

institute: MIT / Broad Institute

description: Untreated Hpx- E coli cells at 60 min

hyb_protocol: Fragmented, biotinylated cDNAs were combined with hybridization cocktail and hybridized to Affymetrix arrays for 16-18 hours at 45 ºC and 60 rpm.

scan_protocol: Arrays were washed and stained on Affymetrix Fluidics Station 450s using the appropriate Affymetrix protocol. The stained arrays were scanned at 532 nm using an Affymetrix GeneChip Scanner 3000.

data_processing: CEL files for the resulting expression profiles were background adjusted and RMA normalized using RMAExpress. Statistical analysis was performed in MATLAB.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Untreated Hpx- E coli cells at 60 min

label_protocol: cDNAs were prepared from 10 µg total RNA through a random primed reverse transcription using SuperScript II (Invitrogen, Carlsbad, CA). The RNAs were digested with the addition of 1M NaOH and incubation at 65ºC for 30 minutes. The mixtures were neutralized with the addition of 1M HCl. The cDNAs were purified using QIAquick MinElute PCR purification columns (Qiagen, Valencia, CA), following the manufacturer’s protocol. The cDNAs (3 – 5 μg) were fragmented to a size range of 50-200 bases with DNase I (0.6 U/ μg cDNA) at 37 ºC for 10 minutes followed by inactivation of the enzyme at 98 ºC for 10 minutes.

growth_protocol: Cells were grown in 10 mL LB in 250 mL baffled flasks at 37°C and 300 RPM in a light-protected, humidity-controlled incubator shaker to an OD600 of ~0.3 before transfer to 14 mL polypropylene tubes and indicated treatments applied.

extract_protocol: Total RNA was obtained using RNAprotect (Qiagen), the RNeasy Protect Bacteria Mini Kit (Qiagen) and Turbo DNA-free (Life Technologies) DNase treatment according to respective manufacturer instructions.

treatment_protocol: Cells were treated with their respective treatments for 1 hour before sample collection for RNA extraction.

value: ∆ahpCF ∆katE ∆katG

value: untreated

tag: timing

value: 0 min


title: UC Sample 60


title: Hpx KO Untreated 2

description: Untreated Hpx- E coli cells at 60 min

tag: treatment


title: NG OF CONTROL 1 MICE

description: control replicate 1

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


title: Fur KO Gent 3

description: Gent treated ∆fur E coli cells at 60 min

tag: genotype

value: ∆fur

value: 5 ug/ml gentamicin

value: 60 min


title: UC Sample 58

value: Female


title: Hpx KO Untreated 1

description: Untreated Hpx- E coli cells at 60 min


title: Fur KO Gent 2

source_name: Gent treated ∆fur E coli cells at 60 min


title: UC Sample 132

value: Chinese


title: UC Sample 135

value: Male


title: UC Sample 136

value: Indian


title: UC Sample 131


title: UC Sample 56


title: UC Sample 128


title: UC Sample 130


title: UC Sample 57


title: UC Sample 59


title: Fur KO Gent 1


title: UC Sample 54

value: Malay


title: UC Sample 55


title: UC Sample 133


title: UC Sample 134


title: UC Sample 126


title: Fur KO Untreated 3

description: Untreated ∆fur E coli cells at 60 min

source_name: Untreated ∆fur E coli cells at 60 min


title: UC Sample 125


title: Fur KO Untreated 2

description: Untreated ∆fur E coli cells at 60 min


title: UC Sample 123


title: UC Sample 53


title: UC Sample 52


title: UC Sample 122


title: UC Sample 127


title: UC Sample 124


title: Fur KO Untreated 1

description: Untreated ∆fur E coli cells at 60 min


title: UC Sample 51


title: WT H2O2 2

description: H2O2 treated WT E coli cells at 60 min

source_name: H2O2 treated WT E coli cells at 60 min

value: WT

value: 10 uM H2O2


title: UC Sample 118


title: UC Sample 129


title: UC Sample 117


title: UC Sample 121


title: UC Sample 116


title: WT H2O2 1

description: H2O2 treated WT E coli cells at 60 min


title: UC Sample 48


title: UC Sample 50


title: UC Sample 49


title: UC Sample 120


title: UC Sample 119


title: UC Sample 113


title: WT H2O2 3

description: H2O2 treated WT E coli cells at 60 min


title: UC Sample 115


title: WT Nor 2

description: Nor treated WT E coli cells at 60 min

source_name: Nor treated WT E coli cells at 60 min

value: 250 ng/ml norfloxacin


title: WT Nor 3

description: Nor treated WT E coli cells at 60 min


title: UC Sample 47


title: UC Sample 46


title: WT Nor 1

description: Nor treated WT E coli cells at 60 min


title: UC Sample 112


title: UC Sample 111


title: UC Sample 44


title: WT Kan 3

description: Kan treated WT E coli cells at 60 min

source_name: Kan treated WT E coli cells at 60 min

value: 5 ug/ml kanamycin


title: UC Sample 108


title: UC Sample 109


title: UC Sample 114


title: UC Sample 45


title: WT Kan 2

description: Kan treated WT E coli cells at 60 min


title: UC Sample 106


title: UC Sample 43


title: UC Sample 110


title: UC Sample 107


title: UC Sample 102


title: UC Sample 41


title: WT Gent 3

description: Gent treated WT E coli cells at 60 min

source_name: Gent treated WT E coli cells at 60 min


title: WT Gent 2

description: Gent treated WT E coli cells at 60 min


title: UC Sample 40


title: WT Kan 1

description: Kan treated WT E coli cells at 60 min


title: UC Sample 42


title: UC Sample 101


title: UC Sample 93


title: UC Sample 99


title: UC Sample 98


title: UC Sample 100


title: WT Amp 3

description: Amp treated WT E coli cells at 60 min

source_name: Amp treated WT E coli cells at 60 min

value: 5 ug/ml ampicillin


title: UC Sample 103


title: UC Sample 97


title: UC Sample 96


title: UC Sample 39


title: UC Sample 95


title: UC Sample 37


title: WT Amp 2

description: Amp treated WT E coli cells at 60 min


title: WT Amp 1

description: Amp treated WT E coli cells at 60 min


title: UC Sample 90


title: UC Sample 105


title: UC Sample 35


title: UC Sample 88


title: UC Sample 34


title: UC Sample 36


title: UC Sample 87


title: UC Sample 86


title: UC Sample 104


title: WT Untreated 2

description: Untreated WT E coli cells at 60 min

source_name: Untreated WT E coli cells at 60 min


title: UC Sample 38


title: UC Sample 33


title: UC Sample 92


title: UC Sample 94


title: UC Sample 89


title: UC Sample 85


title: UC Sample 91


title: UC Sample 83


title: WT Gent 1

description: Gent treated WT E coli cells at 60 min


title: WT Untreated 1

description: Untreated WT E coli cells at 60 min


title: UC Sample 82


title: WT Untreated 3

description: Untreated WT E coli cells at 60 min


title: UC Sample 84


title: UC Sample 81


title: Anaplastic thyroid carcinoma - biological replicate 5

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

hyb_protocol: Performed according to manufacturer's instructions (Affymetrix) for Affymetrix Mouse Gene 1.0 ST arrays.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G; GeneChip® Command Console.

data_processing: Raw hybridization intensities from Affymetrix Mouse Gene 1.0 ST arrays were normalized and summarized using the Affymetrix Power Tools software package (Affymetrix Inc., Santa Clara, CA.) to derive gene-level expression estimates (rma-sketch, MoGene-1_0-st-v1.r4.pgf, MoGene-1_0-st-v1.r4.clf, MoGene-1_0-st-v1.r4.bgp, MoGene-1_0-st-v1.r4.mps, MoGene-1_0-st-v1.r4.qcc).  Multiple probe-sets targeting the same gene were collapsed using their median value. Differential gene expression analysis was performed using the Bioconductor package limma (Smyth GK, 2005) in the R environment for statistical computing (http://www.R-project.org).

source_name: Murine Anaplastic Thyroid Carcinoma (ATC) tumors

label_protocol: Affymetrix GeneChip® WT Sense Target Labeling.

extract_protocol: RNA was extracted using Qiazol (Qiagen).

tag: tumor histology

value: TPOCreER; BrafV600E; p53 -/- anaplastic thyroid carcinoma - biological replicate 5

tag: strain

value: mixed C57BL/6;129SvJae


title: Anaplastic thyroid carcinoma - biological replicate 4

value: Murine Anaplastic Thyroid Carcinoma (ATC) tumors

value: TPOCreER; BrafV600E; p53 -/- anaplastic thyroid carcinoma - biological replicate 4


title: Anaplastic thyroid carcinoma - biological replicate 3

value: TPOCreER; BrafV600E; p53 -/- anaplastic thyroid carcinoma - biological replicate 3


title: UC Sample 74

source_name: Umbilical cord


title: Anaplastic thyroid carcinoma - biological replicate 2

value: TPOCreER; BrafV600E; p53 -/- anaplastic thyroid carcinoma - biological replicate 2


title: UC Sample 79


title: UC Sample 32

hyb_protocol: Standard Illumina hybridization protocol


title: UC Sample 29


title: UC Sample 30


title: UC Sample 78


title: Anaplastic thyroid carcinoma - biological replicate 1

value: TPOCreER; BrafV600E; p53 -/- anaplastic thyroid carcinoma - biological replicate 1


title: UC Sample 75


title: UC Sample 28


title: UC Sample 27

value: Female


title: UC Sample 72


title: UC Sample 73


title: UC Sample 80

value: Chinese


title: UC Sample 26


title: Papillary thyroid carcinoma - biological replicate 5

source_name: Murine Papillary Thyroid Carcinoma (PTC) tumors

value: TPOCreER; BrafV600E papillary thyroid carcinoma - biological replicate 5


title: UC Sample 71


title: Papillary thyroid carcinoma - biological replicate 4

value: Murine Papillary Thyroid Carcinoma (PTC) tumors

value: TPOCreER; BrafV600E papillary thyroid carcinoma - biological replicate 4


title: UC Sample 77

value: Indian


title: Papillary thyroid carcinoma - biological replicate 3

value: TPOCreER; BrafV600E papillary thyroid carcinoma - biological replicate 3


title: UC Sample 70

value: Male

value: Malay


title: UC Sample 69


title: UC Sample 68


title: UC Sample 31


title: UC Sample 24


title: UC Sample 76


title: UC Sample 64


title: Papillary thyroid carcinoma - biological replicate 2

value: TPOCreER; BrafV600E papillary thyroid carcinoma - biological replicate 2


title: UC Sample 25


title: UC Sample 67


title: UC Sample 22


title: UC Sample 23


title: UC Sample 66


title: Papillary thyroid carcinoma - biological replicate 1

value: TPOCreER; BrafV600E papillary thyroid carcinoma - biological replicate 1


title: UC Sample 65


title: UC Sample 21


title: UC Sample 61


title: UC Sample 63


title: UC Sample 62


title: UC Sample 60


title: UC Sample 20


title: UC Sample 57


title: EPC-Control miRNA

city: Taipei City

first: Tse-Shun

last: Huang

address: No.155, Sec.2, Linong Street

department: Institute of Microbiology and Immunology

institute: National Yang-Ming University

hyb_protocol: Agilent miRNA Microarray System

scan_protocol: Agilent Microarray Scanner, Cy3 Channel Laser Power: 100, Cy3 Channel PMT setting: Hi 100%_Lo 5%, Apply XDR: Yes, Detector Gain: 1, Scans: 1, Scan Speed: 25, Pixel Resolution: 5 microns

data_processing: Raw data are processed with R/Bioconductor AgiMicroRna package and normalized with RMA algorithm.

source_name: PB-EPC, High glucose, Control

label_protocol: Agilent's miRNA microarray system v2.2

growth_protocol: PB-EPC were maintained in Endothelial growth medium 2 (Lonza)

extract_protocol: Total RNA was extracted by Qiagen miRNeasy kit according to the manufacturer's instructions.

treatment_protocol: PB-EPC were seeded  in Endothelial growth medium 2 with 25mM glucose for 48 hours prior to 30 minute far infrared exposure.

tag: cell type

value: Endothelial precursor cell

value: Control


title: UC Sample 58


title: UC Sample 18


title: EPC-FIR miRNA

source_name: PB-EPC, High glucose, FIR treated

value: Far Infrared


title: UC Sample 56


title: UC Sample 17


title: UC Sample 54


title: UC Sample 19


title: UC Sample 55


title: UC Sample 16


title: UC Sample 53


title: UC Sample 50


title: UC Sample 51


title: UC Sample 59


title: UC Sample 14


title: UC Sample 52


title: UC Sample 48


title: UC Sample 13


title: UC Sample 49


title: UC Sample 15


title: UC Sample 46


title: UC Sample 45


title: UC Sample 41


title: UC Sample 12


title: UC Sample 47


title: UC Sample 42


title: HepG2_rep1

city: Taichung

first: Wei-Chien

address: 9F, No.6, Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

institute: China Medical University

description: microRNA expression in HepG2x cells

hyb_protocol: A miRNA Hybridization Buffer (Ambion) was added to the fluorescently labeled miRNAs and the solution was heated (95ºC) for 3 min. Slides were hybridized form 12 to 16 h at 42 ºC in sealed cassettes using a water bath. Following hybridization, the slides were washed and dried prior to a high-resolution scan.

scan_protocol: Scan on a GenePix 4000B (Axon Instruments, CA, USA). Raw data were normalized and analyzed using Array-Pro Analyzer Version 4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA).

data_processing: We calculated net intensity by subtracting the mean intensity of all pixels within the local background area from the mean intensity of all pixels within the spot areas, and normalizd the data according to global Variance Stabilization Normalization (VSN) procedure.

source_name: HepG2x cells

label_protocol: mirVanaTM miRNA Labeling Kit (Ambion) and amine-reactive dyes as recommended by the manufacturer.

growth_protocol: Hep3B, HepG2, and their HBx-expressing transfectant were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/F12

extract_protocol: To isolate miRNA fractions from total RNA, 100μｇ total RNA was fractionated and cleaned up with the flashPAGETM fractionator System and reagents (Ambion) per the manufacturer’s recommendation.

treatment_protocol: cell lines were transfected with vector or HBx followed by selection with antibotics

tag: cell line

tag: tranfectant

value: HBx


title: UC Sample 11


title: HepG2_parental_rep1

description: microRNA expression in parental HepG2 cells

source_name: HepG2 cells

value: vector


title: UC Sample 35


title: UC Sample 43


title: UC Sample 38


title: Hep3Bx_rep1

description: microRNA expression in Hep3Bx cells

source_name: Hep3Bx cells


title: UC Sample 10


title: UC Sample 36


title: UC Sample 39


title: UC Sample 40


title: UC Sample 9


title: Hep3B_parental_rep1

description: microRNA expression in parental Hep3B cells

source_name: Hep3B cells


title: UC Sample 44


title: UC Sample 34


title: UC Sample 7


title: UC Sample 6


title: UC Sample 8


title: UC Sample 31


title: cortex_adult_treated AV5

city: Perugia

first: Stefano

last: Fiorucci

address: Via E dal Pozzo

department: Dipartimento di Medicina Clinica e Sperimentale

institute: Universita di Perugia

description: adult (22 months) animals, VSL#3 treated

hyb_protocol: The hybridization procedure was performed according to the the “One-Color Microarray-Based Gene Expression Analysis protocol (version 6.5, part number G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 0.6 µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Rat Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) 10.7.3.1 was used to read out and process the microarray image files. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Rosetta error model; Lee Weng et al 2006).

organism: Rattus norvegicus

source_name: cortex

label_protocol: Sample labeling was performed as detailed in the “One-Color Microarray-Based Gene Expression Analysis protocol (version 6.5, part number G4140-90040). Briefly, 100 ng of each total RNA samples was used for the amplification and labeling step using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies). Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Rats were housed 2 per cage and allowed to acclimatize for 1 week following delivery. Body weights and food and water intake were assessed during this time. On each day thereafter, 2 rats per day were assigned to a control or treatment group and received maple syrup either alone or with the probiotic every day over a course of 6 weeks. Stool samples were taken before treatment, mid-way through treatment, and at the end of the treatment period. Six weeks after the onset of treatment, rats were assessed for their ability to sustain LTP in the hippocampus. At the end of the period of electrophysiological recordings, blood samples were taken (for metabolomics analysis) and brain tissue was harvested for microarray analysis of the cortex.

extract_protocol: Rat total RNA was isolated  from rat cortex samples by using standard RNA extraction protocols (Trizol). RNA quality and integrity were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified by measuring A260nm on the ND-1000 Spectrophotometer (NanoDrop Technologies).

value: Han Wistar

value: brain cortex

tag: age

value: adult


title: UC Sample 33

value: Chinese