title: Y4184snf1_47

description: This sample is of Yarrowia lipolytica Y4184 snf1 mutant. It is the third of three iological replicates used in this experiment, each from separate cultures.


title: Y4184Ura+ control2

status: Public on Sep 25 2013

type: RNA

city: Wilmington

first: Seung-Pyo

last: Hong

state: DE

address: Experimental Station, E328/B47B

department: BCS&E

country: USA

institute: DuPont Central Research and Development

description: This sample is of Yarrowia lipolytica Y4184Ura+ control. It is the second of three biological replicates used in this experiment, each from separate cultures.

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

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

data_processing: Data were normalized using RMA, and then averaged over the 4 replicated probes.

molecule: total RNA

organism: Yarrowia lipolytica

source_name: Yarrowia lipolytica Y4184URA+ control

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

growth_protocol: Yarrowia lipoltica Y4184 strains were grown to mid-log phase (O.D.600nm 2.0) anerobically at 30°C in synthetic dextrose medium (2% glucose, 0.67% Yeast Nitrogen base without amino acids and with ammonium sulfate).

extract_protocol: A 10 ml aliquot from each culture was harvested by centrifugation at 2,000 x g for 2 min. The cell pellet was immediately frozen in liquid nitrogen and stored at -80 ˚C. Total RNA was prepared from cell pellets using TRIzol reagent (Life Technologies, Carlsbad, CA). Cell breakage was carried out using a Mini-Beadbeater 8 (BSP, Bartlesville, OK). The extracted total RNA was then purified using a Qiagen RNeasy kit.

treatment_protocol: Yarrowia lipoltica Y4184 snf1 strains were grown to mid-log phase (O.D.600nm 2.0) anerobically at 30°C in synthetic dextrose medium (2% glucose, 0.67% Yeast Nitrogen base without amino acids and with ammonium sulfate).

tag: genotype/variation

value: Wild-type


title: Y4184snf1_43

description: This sample is of Yarrowia lipolytica Y4184 snf1 mutant. It is the first of three biological replicates used in this experiment, each from separate cultures.

source_name: Yarrowia lipolytica Y4184 delta_snf1

value: snf1 deletion


title: Y4184Ura+ control1

description: This sample is of Yarrowia lipolytica Y4184Ura+ control. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: control

city: sendai

first: yosuke

last: shimodaira

address: 1-1, seiryomachi, aoba-ku

country: Japan

institute: tohoku university

description: Control

data_processing: The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package

label: SYBR Green

organism: Homo sapiens

label_protocol: PCR assays were performed using the tg-treated and non-treated HT29 cells using PCR assay panel (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from total RNA using theSuperscriptⅢreverse transcriptase (Invitrogen). Quantitative real-time PCR were performed using StepOnePlus.

extract_protocol: Total RNA was extracted with Illustra RNAspin  followed by DNase I treatment.

tag: cell line

tag: treatment

value: control


title: tg treated cells

description: Test

value: thapsigargin


title: Y4184Ura+ control3

description: This sample is of Yarrowia lipolytica Y4184Ura+ control. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: Breast tumor [P198T]

status: Public on Sep 24 2013

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

description: Breast tumor

data_processing:
Raw data were processed by REST2009 software according to Pfaffl et al Nucleic Acids Res. 2000;30: e36.
For the normalization it uses the average of four housekeeping genes: EIF2B1, MRPL19, IPO8, and UBB
Target gene signals normalized to housekeeping genes; 2^-ΔCt, where -ΔCt = -(Ct_Target − Ct_HKG)
Raw data were processed by REST2009 software according to Pfaffl et al Nucleic Acids Res. 2000;30: e36.

label: FAM

source_name: Breast tumor

label_protocol: cDNA was synthesized using 0.5 µg of total RNA by help of RevertAidTM First Strand cDNA Synthesis Kit with random hexamer primers according to manufacturer´s protocol (MBI Fermentas, Vilnius, Lithuania) and stored at -80 oC. qPCR was performed in RotorGene 6000 produced by Corbett Research (Sydney, Australia) with 45 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds. cDNA was preamplified using TaqMan PreAmp Master Mix (Life Technologies Corp., Carlsbad, CA, USA).

extract_protocol: Total RNA was isolated from frozen tissues using Trizol reagent according to manufacturers protocol (Invitrogen, Carlsbad, CA, USA)

tag: tissue

value: Tumor


title: Breast tumor [P166T]

description: Breast tumor


title: Paired non-neoplastic tissue [P181N]

description: Paired non-neoplastic tissue

source_name: Paired non-neoplastic tissue

value: Control


title: Breast tumor [P181T]

description: Breast tumor


title: Paired non-neoplastic tissue [P198N]

description: Paired non-neoplastic tissue


title: 8DKD_rep2

city: Dallas

first: Peter

last: Michaely

state: TX

address: 5323 Harry Hines Blvd.

department: Cell Biology

institute: UT Southwestern Medical Center

description:
Replicate 2
7196763065_C

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization with IlluminaGUI

label: biotin

source_name: SV589_8Day KD

label_protocol: Biotin labeling was performed using TargetAmp-Nano (Illumina)

growth_protocol: Cells (SV40 immortalized primary human fibroblasts) were depleted of cavin-3 for 0, 3 or 8 days. This depletion was achieved by transfecting cavin-3 siRNA at day 0 and day 5 when cells were split. Media was replaced one day prior to the end of the experiment for cells that were serum starved.

extract_protocol: RNA was isolated using RNeasy (Qiagen) according to the manufacturer's instructions. RNA quality was validated by BioAnalyzer Chip (Illumina)

treatment_protocol: On day of experiment cells were either untreated, treated with 100 ng/ml EGF for 1 hr or treated with 100 ng/ml EGF for 3 hr.

tag: knockdown (days)

value: no treatment


title: 8hrs Dasatinib Rep3

city: San Francisco

first: Neil

last: Shah

address: 513 Parnassus

institute: UCSF

description: Replicate 3

data_processing: Data was adjusted and normalized using the lumi pipeline (PMID: 18467348).

label: Biotin

source_name: CML Cell Line

label_protocol: Biotinylated cRNA was prepared using the Ambion Illumina TotalPrep RNA Amplification kit.

growth_protocol: K562 cells were propogated in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (FBS, Omega Scientific), L-glutamine (1%) and penicillin/streptomycin (1%) (Invitrogen).

extract_protocol: Total cellular RNA was extracted using the Qiagen RNeasy kit with Dnase I treatment.  RNA integrity was assessed on a Bioanalyzer using the Agilent RNA 6000 Nano Kit and cRNA was generated using the Ambion Illumina TotalPrep RNA Amplification kit.

treatment_protocol: K562 cells were treated with 0.2% DMSO or 100nM dasatinib in RPMI 1640 medium (0.1% FBS) for the indicated amount of time prior to cell lysis and RNA extraction.

tag: time

tag: disease

value: CML

value: 100nM Dasatinib


title: 8DKD

description:
Replicate 1
6303256037_C


title: 3DKD

description:
Replicate 1
6303256037_B


title: NoKD_rep3

description:
Replicate 3
7196763074_A


title: 8hrs Dasatinib Rep2

description: Replicate 2


title: 3DKD_rep2

description:
Replicate 2
7196763065_B

source_name: SV589_3Day KD


title: 24hrs DMSO Rep1

description: Replicate 1

value: 0.2% DMSO


title: 24hrs DMSO Rep2

description: Replicate 2


title: 3DKD_rep3

description:
Replicate 3
7196763074_B


title: 24hrs Dasatinib Rep2

description: Replicate 2


title: 4hrs Dasatinib Rep3

description: Replicate 3


title: NoKD

description:
Replicate 1
6303256037_A


title: 24hrs Dasatinib Rep1

description: Replicate 1


title: 8DKD_rep3

description:
Replicate 3
7196763074_C


title: NoKD_rep2

description:
Replicate 2
7196763065_A


title: 8hrs Dasatinib Rep1

description: Replicate 1


title: 15DKD_SerumStarved->3hrEGF_rep1

description:
Replicate 1
7196763065_L

source_name: SV589_15Day KD_Serum Starved -> 3hr EGF

value: Serum Starved; 3h EGF


title: 4hrs Dasatinib Rep1

description: Replicate 1


title: 24hrs Dasatinib Rep3

description: Replicate 3


title: 15KD_rep2

description:
Replicate 2
7196763074_D

source_name: SV589_15Day KD


title: 15DKD_rep1

description:
Replicate 1
7196763065_D


title: 15DKD_SerumStarved->3hrEGF_rep2

description:
Replicate 2
7196763074_L


title: 4hrs Dasatinib Rep2

description: Replicate 2


title: 24hrs DMSO Rep3

description: Replicate 3


title: 15KD_SerumStarved->1hrEGF_rep1

description:
Replicate 1
7196763032_J

source_name: SV589 15 Day KD Serum Starved-> 1hr EGF

value: Serum Starved; 1h EGF


title: 15KD_SerumStarved->1hrEGF_rep3

description:
Replicate 3
7196763032_L


title: 15KD_SerumStarved_rep1

description:
Replicate 1
7196763065_H

source_name: SV589_15Day KD_Serum Starved

value: Serum Starved; no EGF


title: 15KD_SerumStarved->1hrEGF_rep2

description:
Replicate 2
7196763032_K


title: Control_15

type: other

city: Oberlin

first: Jordan

last: Price

state: OH

address: 119 Woodland St

institute: Oberlin College

description:
IgG
Median Fluorescence intensity (MFI) of 635 (Cy5) channel minus local background

hyb_protocol: Serum was diluted 1:250 from stocks (maintained at -80 deg. C. in) in PBS + 0.5% Tween 20 (Sigma-Aldrich, St. Louis, MO) and 2.5% fetal calf serum (Omega Scientific, Tarzana CA). Post primary incubation, washed arrays were incubated with 0.375ug/ml Goat anti-Human IgG conjugated to Cy5 (Jackson Immunoresearch, West Grove, PA).

scan_protocol: Arrays were scanned using an Axon digital scanning system (Molecular Devices, Sunnyvale, CA)

data_processing: Array images were analyzed using GenePix 6.0 software (Molecular Devices)

molecule: other

source_name: serum

tag: interferon signature


title: Control_13

label: Goat anti-Human IgG conjugated to Cy5 (Jackson Immunoresearch, West Grove, PA)


title: Control_11


title: 8DKD_SerumStarved->3hrEGF_rep2

description:
Replicate 2
7196763074_K

source_name: SV589_8Day KD_Serum Starved -> 3hr EGF


title: Control_12


title: Control_8


title: Control_10


title: Control_9


title: 8DKD_SerumStarved->3hrEGF_rep1

description:
Replicate 1
7196763065_K


title: 8DKD_SerumStarved->1hrEGF_rep2

description:
Replicate 2
7196763032_G

source_name: SV589 8 Day KD Serum Starved-> 1hr EGF


title: Control_14


title: Control_5


title: 8DKD_SerumStarved->1hrEGF_rep4

description:
Replicate 4
7196763032_I


title: MCF10A_T58A_rep1

city: Toronto

first: Michelle

last: Chan-Seng-Yue

address: 101 College Street

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Samples were hybridized to GeneChip Human Genome U133 Plus 2.0 Arrays according to the standard Affymetrix protocol.

scan_protocol: Scanned with GeneChip scanner 3000 7G.

data_processing: The data was pre-processed using the RMA algorithm from the affy (v1.30.0) package for R (v2.13.2) and updated Entrez Gene annotations (hgu133plus2hsentrezgcdf_14.0.0).

source_name: MCF10A T58A mutant, day 4

label_protocol: Samples were prepared according to the standard Affymetrix protocol from 8 ug total RNA.

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

value: T58A mutant


title: MCF10A_Myc_rep3

source_name: MCF10A Myc, day 4

value: Myc


title: MCF10A_Myc_rep1


title: 8DKD_SerumStarved_rep2

description:
Replicate 2
7196763065_G

source_name: SV589_8Day KD_Serum Starved


title: 8DKD_SerumStarved->1hrEGF_rep3

description:
Replicate 3
7196763032_H


title: 3DKD_SerumStarved->3hrEGF_rep1

description:
Replicate 1
7196763065_J

source_name: SV589_3Day KD_Serum Starved -> 3hr EGF


title: 8DKD_SerumStarved_rep3

description:
Replicate 3
7196763074_G


title: MCF10A_T58A_rep2


title: Control_4


title: 3DKD_SerumStarved->3hrEGF_rep2

description:
Replicate 2
7196763074_J


title: Control_7


title: 3DKD_SerumStarved->1hrEGF_rep4

description:
Replicate 4
7196763032_F

source_name: SV589 3 Day KD Serum Starved-> 1hr EGF


title: MCF10A_T58A_rep3


title: Control_6


title: 8DKD_SerumStarved_rep1

description:
Replicate 1
6303256037_F


title: 8DKD_SerumStarved->1hrEGF_rep1

description:
Replicate 1
6303256039_L

source_name: SV589_8DayKD_SerumStarved->1hr EGF


title: IFN-low SLE_13

value: IFN low


title: Control_3


title: IFN-low SLE_14


title: Control_1


title: Control_2


title: IFN-low SLE_15


title: IFN-low SLE_11


title: IFN-low SLE_8


title: IFN-low SLE_9


title: IFN-low SLE_10


title: IFN-low SLE_7


title: IFN-low SLE_6


title: IFN-low SLE_12


title: IFN-low SLE_5


title: MCF10A_S71AS81A_rep2

source_name: MCF10A S71A/S81A mutant, day 4

value: S71A/S81A mutant


title: MCF10A_GFP_rep3

source_name: MCF10A GFP control, day 4

value: GFP control


title: 15KD_SerumStarved_rep2

description:
Replicate 2
7196763074_H


title: MCF10A_Myc4A_rep3

source_name: MCF10A Myc4A mutant, day 4

value: Myc4A mutant


title: MCF10A_Myc4A_rep2


title: 3DKD_SerumStarved->1hrEGF_rep3

description:
Replicate 3
7196763032_E


title: IFN-low SLE_4


title: 3DKD_SerumStarved_rep3

description:
Replicate 3
7196763074_F

source_name: SV589_3Day KD_Serum Starved


title: IFN-high SLE_15

value: IFN high


title: IFN-low SLE_2


title: MCF10A_Myc_rep2


title: 3DKD_SerumStarved->1hrEGF_rep2

description:
Replicate 2
7196763032_D


title: MCF10A_S71AS81A_rep1


title: IFN-low SLE_1


title: 3DKD_SerumStarved->1hrEGF_rep1

description:
Replicate 1
6303256037_H

source_name: SV589_3DayKD_SerumStarved->1hr EGF


title: IFNg_neg_5

tag: anti-ifn-gamma

value: Individual previously observed not to have IgG autoantibodies targeting IFNg


title: IFN-high SLE_13


title: IFNg_neg_4


title: 3DKD_SerumStarved_rep1

description:
Replicate 1
6303256037_E


title: IFN-high SLE_14


title: MCF10A_GFP_rep2


title: IFN-high SLE_12


title: IFN-low SLE_3


title: IFNg_neg_3


title: NoKD_SerumStarved->3hrEGF_rep2

description:
Replicate 2
7196763074_I

source_name: SV589_NoKD_Serum Starved -> 3hr EGF


title: MCF10A_S71AS81A_rep3


title: IFNg_neg_2


title: MCF10A_Myc4A_rep1


title: IFN-high SLE_11


title: NoKD_SerumStarved->1hrEGF_rep4

description:
Replicate 4
7196763032_C

source_name: SV589 NoKD Serum Starved-> 1hr EGF


title: IFN-high SLE_10


title: IFNg_neg_1


title: EV71_PBMC_10DPI

city: Kunming

first: Ying

last: Zhang

state: Yunnan

address: 935 Jiaoling Rd.

country: China

institute: Institute of Medical Biology, Chinese Academy of Medicine Science

description: Gene expression after 10 day in rhesus neonates PBMC

hyb_protocol: Each slide was hybridized with 1.65 Î¼l of Cy3-labeled cRNA using the Gene Expression Hybridization Kit (Agilent) in a Hybridization Oven (Agilent). After 17 hours of hybridization, slides were washed in staining dishes (Thermo, MA, USA) with the Gene Expression Wash Buffer Kit (Agilent). Briefly, 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-026806 M. mulatta (Rhesus) Oligo Microarray v2 for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with the Gene Expression Wash Buffer Kit (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Macaca mulatta

source_name: PBMC, 10dpi

label_protocol: mRNA purified from total RNA after removal of rRNA was amplified and transcribed into fluorescent cRNA using the manufacturer’s Low Input Quick Amp Labeling protocol (Agilent). Labeled cRNA was purified using the RNeasy Mini Kit (QIAGEN, GmBH, Germany). Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA from the PBMCs using TRIzol Reagent (Invitrogen, CA, USA) and purified using RNeasy Mini Kit (QIAGEN, GmBH, Germany). The RNA Integrity Number (RIN) was also evaluated to inspect RNA integrity using an Agilent Bioanalyzer 2100 (Agilent, CA, USA).

treatment_protocol: Freshly peripheral blood from experiment or control monkeys was sampled, then was isolated the PBMCs.

value: PBMC

tag: time point

value: 10 days after Enterovirus 71 infection


title: IFN-high SLE_9

source_name: serum


title: NoKD_SerumStarved->3hrEGF_rep1

description:
Replicate 1
7196763065_I


title: NoKD_SerumStarved->1hrEGF_rep3

description:
Replicate 3
7196763032_B


title: IFNg_pos_5

value: Individual previously observed to have IgG autoantibodies targeting IFNg


title: MCF10A_GFP_rep1


title: IFN-high SLE_8


title: NoKD_SerumStarved->1hrEGF_rep1

description:
Replicate 1
6303256037_G

source_name: SV589_NoKD_SerumStarved->1hr EGF


title: EV71_PBMC_7DPI

description: Gene expression after 7 day in rhesus neonates PBMC

source_name: PBMC, 7dpi

value: 7 days after Enterovirus 71 infection


title: 3DKD_SerumStarved_rep2

description:
Replicate 2
7196763065_F


title: IFNg_pos_4


title: EV71_PBMC_C

description: Gene expression in rhesus neonates PBMC

source_name: PBMC, control


title: IFNg_pos_3


title: IFN-high SLE_7


title: IFN-high SLE_6


title: NoKD_SerumStarved->1hrEGF_rep2

description:
Replicate 2
7196763032_A


title: IFNg_pos_1


title: IFNg_pos_2


title: IFN-high SLE_4


title: NoKD_SerumStarved_rep2

description:
Replicate 2
7196763065_E

source_name: SV589_NoKD_Serum Starved


title: HepG2_cells_5000nM-RVX-208-treatment_4h_replicate_1

city: Oxford

first: Panagis

last: Filippakopoulos

state: Oxfordshire

address: ORCRB - Roosevelt Drive

department: Nuffield Department of Medicine

country: United Kingdom

institute: Oxford University

description:
Sample name: RVX1
Gene expression data from HepG2 cells treated with 5000nM RVX-208 for 4h

hyb_protocol: Affymetrix GeneChip® Human Gene 1.0 ST arrays were hybridized for 17h to 11 mg of labeled, amplified cDNA, washed, stained and scanned according to the protocol described in WT Sense Target Labeling Assay Manual

scan_protocol: Chips were processed on an Affymetrix GeneChip Fluidics Station 450 and Scanner 3000

data_processing: The Affymetrix Command Console (v.3.2.4; Affymetrix) was used to generate CEL files. Raw CEL data were processed in R (v.2.15.3) using Bioconductor (v.2.11) and the simpleaffy package (v.2.34.0). Quality controls were carried out using the arrayQualityMetrics package (v.3.14.0) taking into account array intensity distributions, distance between arrays and variance mean-dependence. Principal component analysis was used to decide which arrays to process together. On this basis one of the three arrays treated with JQ1 was considered to be an outlier and was discarded (sample 'JQ3', file 'JQ3_(HuGene-1_0-st-v1).cel'), with the rest of the analysis performed without taking it into account. Background correction and normalization were carried out employing the Robust Multichip Array (RMA) method implemented in the affyPLM package (v.1.34.0). Data were filtered using the genefilter package (v.1.40.0) and probe sets that did not have an Entrez gene identifier were removed. From the 32321 probe sets available on the Human Gene 1.0 ST chip, 19816 remained after filtering. A linear model was applied employing the limma package (v.3.14.4) followed by empirical Bayesian analysis to determine differential expression between not-treated and treated samples. Data were annotated using the hugene10sttranscriptcluster.db annotation data (http://www.bioconductor.org/packages/2.11/data/annotation/html/hugene10sttranscriptcluster.db.html).

source_name: HepG2 cells, RVX-208 treatment (5000nM), 4h

label_protocol: 200ng of total RNA were amplified and labelled using the Ambion WT expression kit and the Affymetrix GeneChip WT Terminal Labelling and Controls Kit

growth_protocol: HepG2 cells (ATCC: HB-8065) were maintained in α-MEM (Cat.#BE12-169F; BioWhittaker) supplemented with 10 % heat-inactivated foetal calf serum (PAA #A15-152), non-essential amino acids (Cat. #M7145; Sigma), glutamine (Cat.#M11-004; PAA), and vitamins (Cat.#M6895; Sigma). Cells were grown at 37 °C in a humidified cabinet at 5 % CO2 (Heraeus Function Line). For experiments, cells were seeded the day prior to treatment at 2x105/ml. Treatments were performed for 4 h so that a final concentration of 0.1 % DMSO (Cat.#D1435; Sigma) was achieved. At harvest, cells were washed once with PBS (Cat.#H15-002; PAA), and lysed in situ using RLT buffer supplemented with 10 μl/ml β-mercaptoethanol (Cat.#M7522; Sigma).

extract_protocol: Total RNA was extracted and prepared using RNeasy columns (Cat.#74106 plus; Qiagen) including a Qia shredding step (Cat.#79656; Qiagen) and an on-column DNAse digestion (Cat.#EN0521; Fermentas), according to the manufacturer’s instructions

treatment_protocol: Cells were treated for 4h with (1) DMSO or (2) 500nM JQ1 or (3) 5000nM RVX-208

tag: agent


title: NoKD_SerumStarved_rep3

description:
Replicate 3
7196763074_E


title: Eed KO BM LT-HSC, biological rep3

city: Boston

first: Huafeng

last: Xie

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: BM LT-HSC Eed KO-3

hyb_protocol: overnight at 45°C

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Data were processed with GenePattern (ExpressionFileCreator, V11), RMA, median scaling

organism: Mus musculus

source_name: Eed KO BM LT-HSC

label_protocol: cDNA is prepared from total RNA using a DNA/RNA chimeric primer and a reverse transcriptase and amplified using SPIA™ amplification. After purification cDNA is fragmented and labeled with Biotin.

growth_protocol: Animals were maintained in the animal facility at Boston Children’s Hospital

extract_protocol: Total RNA was isolated using the RNeasy Micro Plus Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: total BM cells were stained with antibodies and LT-HSCs were sorted directly into RLT Plus buffer summplemented with 1% 2-mercaptoethanol

tag: strain background

value: Mixed; mostly C57BL/6 with some 129S/SvImJ (from CJ7 ES cells).

value: Eed KO

tag: age

value: 9-day old

value: bone marrow

tag: cell type

value: long-term hematopoietic stem cells (LT-HSC)


title: HepG2_cells_5000nM-RVX-208-treatment_4h_replicate_3

description:
Sample name: RVX3
Gene expression data from HepG2 cells treated with 5000nM RVX-208 for 4h


title: Control_7

value: Healthy control


title: EV71_PBMC_4DPI

description: Gene expression after 4 day in rhesus neonates PBMC

source_name: PBMC, 4dpi

value: 4 days after Enterovirus 71 infection


title: IFN-high SLE_3


title: HepG2_cells_5000nM-RVX-208-treatment_4h_replicate_2

description:
Sample name: RVX2
Gene expression data from HepG2 cells treated with 5000nM RVX-208 for 4h


title: Eed KO BM LT-HSC, biological rep1

description: BM LT-HSC Eed KO-1


title: HepG2_cells_500nM-JQ1-treatment_4h_replicate_2

description:
Sample name: JQ2
Gene expression data from HepG2 cells treated with 500nM JQ1 for 4h

source_name: HepG2 cells, JQ1 treatment (500nM), 4h


title: Eed KO BM LT-HSC, biological rep2

description: BM LT-HSC Eed KO-2


title: Control_6


title: NoKD_SerumStarved_rep1

description:
Replicate 1
6303256039_J

value: Serum Starved; no EGF


title: HepG2_cells_DMSO_4h_replicate_3

description:
Sample name: NT3
Gene expression data from HepG2 cells treated with DMSO for 4h

source_name: HepG2 cells, DMSO control, 4h

value: control


title: WT BM LT-HSC, biological rep3

description: BM LT-HSC WT-3

source_name: WT BM LT-HSC

value: wild type


title: IFN-high SLE_5


title: Control_5


title: HepG2_cells_500nM-JQ1-treatment_4h_replicate_1

description:
Sample name: JQ1
Gene expression data from HepG2 cells treated with 500nM JQ1 for 4h


title: WT BM LT-HSC, biological rep2

description: BM LT-HSC WT-2


title: Control_4


title: IFN-high SLE_1


title: IFN-high SLE_2


title: Control_3


title: 21dpi Newt Heart

city: Stockholm

first: Jamie

middle: Ian

last: Morrison

address: Svante Arrheniusväg 20C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

country: Sweden

institute: Stockholm University

description: microRNA reference libraries from homo sapiens, danio rerios and xenopus tropicalis were used on the specified platform.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

organism: Notophthalmus viridescens

source_name: Whole Heart

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 0.5 µg total RNA per sample. The RNA samples were first subject to dephosphorylation reaction to remove 5’ phosphate groups of miRNA molecules. Then an oligonucleotide adapter was added to 3’ end of sample (3’OH containing) RNA sequences using T4 RNA ligase. The adapter sequence contained a tag segment for capturing fluorescent dye during a later dye staining process.

extract_protocol: Total RNA from uninjured and regenerating whole hearts were extracted using the mirVANA miRNA Isolation Kit (Invitrogen). Samples were subsequently treated with a 1/10 volume of 3M Sodium Acetate (pH5.2) and 3X volume of 100% Ethanol prior to shipping to LC Sciences. A total of 2.6, 5.1 and 3.3 micrograms, representing uninjured, 7dpi and 21dpi respectively, were sent for further analysis to LC Sciences.

treatment_protocol: Heart injuries were performed as described in Witman et al., (2011) Developmental Biology. Vol. 354(1):67-76.

tag: developmental stage

value: Adult

tag: stress

value: 21dpi post injury


title: Control_2


title: Uninjured Newt Heart


title: 7dpi Newt Heart

value: 7dpi post injury


title: WT BM LT-HSC, biological rep1

description: BM LT-HSC WT-1


title: HepG2_cells_DMSO_4h_replicate_2

description:
Sample name: NT2
Gene expression data from HepG2 cells treated with DMSO for 4h


title: HepG2_cells_DMSO_4h_replicate_1

description:
Sample name: NT1
Gene expression data from HepG2 cells treated with DMSO for 4h


title: APS1_6

value: Individual with APS-1


title: APS1_7


title: APS1_4


title: Control_1


title: MCF10A-Her2Myc-rep2

city: Sydney

first: Daniel

last: Roden

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute

description: MCF10A cells, Her2 and Myc over-expression

hyb_protocol: Labeled, fragmented cDNA hybridized to Affymetrix Human Gene 1.0 ST Gene Arrays at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

scan_protocol: Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

data_processing: Data was RMA normalised using NormalizeAffymetrixST (version 2.0) GenePattern module from the Peter Wills Bioinformatics Centre's GenePattern Server: http://pwbc.garvan.unsw.edu.au/gp

label_protocol: Total RNA was converted to cDNA. The cDNA was fragmented, biotin labeled at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

growth_protocol: MCF10A cells were cultured at 37°C in 5% CO2 and 95% air to no more than 80% confluence in Dulbecco's modified Eagle's medium/nutrient mixture F-12 medium (Invitrogen, Mulgrave, Vic, Australia) supplemented with 5% (v/v) horse serum (Invitrogen), 20 ng/ml human recombinant EGF (R&D Systems), 0.5 μg/ml hydrocortisone (Sigma), 0.1 ng/ml cholera toxin (Sigma), 10 μg/ml bovine insulin (Sigma), 50 units/ml penicillin G (Invitrogen), and 50 μg/ml streptomycin sulfate (Invitrogen).

extract_protocol: Total RNA was extracted by using the Qiagen RNeasy minikit (Qiagen, Doncaster, Vic, Australia) according to manufacturer’s protocol. Following extraction, RNA concentration and purity were analysed using the NanoDrop® ND-1000 Spectrophotometer (Nano-Drop Technologies, Wilmington, DE, USA). For Affymetrix GeneChip® analysis, the integrity of RNA was analysed using the Agilent Bioanalyser 2100 6000 Nano Assay (Agilent Technologies, Palo Alto, CA, USA) according to the manufacturer’s instructions.

tag: gender

value: female

value: breast

tag: expression

value: Her2 and Myc over-expression


title: MCF10A-Her2Myc-rep3

source_name: MCF10A cells, Her2 and Myc over-expression

tag: cell line


title: MCF10A-Myc-rep1

description: MCF10A cells, Myc over-expression

source_name: MCF10A cells, Myc over-expression

value: Myc over-expression


title: MCF10A-Her2Myc-rep1


title: APS1_3


title: APS1_2


title: MCF10A-Myc-rep2

description: MCF10A cells, Myc over-expression


title: MCF10A-Her2-rep3

description: MCF10A cells, HER2 over-expression

source_name: MCF10A cells, HER2 over-expression

value: HER2 over-expression


title: APS1_5


title: MCF10A-Her2-rep2

description: MCF10A cells, HER2 over-expression


title: MCF10A-Her2-rep1

description: MCF10A cells, HER2 over-expression


title: MCF10A-Vector-rep2

description: MCF10A cells, vector control

source_name: MCF10A cells, vector control


title: Control HEK293 sample1

city: Bethesda

first: Jung

middle: S

last: Byun

state: MD

address: 37 convent drive, Bldg 37,  Rm 1042

institute: NCI/NIH

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 plus 2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: HEK293 cell line, control

label_protocol: Biotinylated cRNA were prepared according to the standard Ambion MessageAmp II Biotin-enhanced protocol from 1 ug total RNA (Message Amp II Biotin-Enhanced Technical Manual, 2006, Ambion).

growth_protocol: HEK293 cells and the cells expressing  HSP70K71E were proliferated with RPMI1640, 10% FBS, 25 mM HEPES, 1X PS

extract_protocol: Total RNA was harvested (RNAeasy kit(Qiagen)/ standard protocol as manufacture recommended) and measured the concentration for mRNA analysis

tag: genotype/variation


title: MCF10A-Vector-rep1

description: MCF10A cells, vector control

tag: tissue


title: MCF10A-Vector-rep3

description: MCF10A cells, vector control


title: HSP70K71E HEK293 sample3

source_name: HEK293 cell line, expressing  HSP70K71E

value: expressing  HSP70K71E


title: Control HEK293 sample2


title: Control HEK293 sample3


title: APS1_1

source_name: serum


title: HSP70K71E HEK293 sample1


title: HSP70K71E HEK293 sample2


title: CBP/p300 KO3, E9.5

city: Saint Louis

first: David

middle: Cy

last: Beebe

state: MO

address: 660 S. Euclid Ave.

department: Ophthalmology and Visual Science

institute: Washington University School of Medicine

description:
7166151072_C
Total RNA amplified as cDNA.

hyb_protocol: Performed using standard Illumina protocol on Illumina Mouse6 v2.0 bead arrays by the Genome Technology Access Center (GTAC) at Washington University.

scan_protocol: Standard Illumina protocol for bead arrays.

data_processing:
Background subtraction and cubic spline normalization and differential expression performed using Illumina Genome Studio software.
Value is the mean hybridization intensity for all beads (usually 25-50 per array) containing the indicated oligonucleotide probe.

source_name: CBP/p300-/- surface ectoderm

label_protocol: The resulting cDNA was biotin labeled using the Illumina biotinylation kit.

growth_protocol: Pregnant mice euthanized and embryos removed at E9.5.

extract_protocol: Total RNA was extracted and purified from the tissue obtained from three mouse embryos. Samples from each genotype were pooled and triplicate samples were amplified using a Qiagen RNeasy Microkit (Qiagen# 74004). Total RNA was amplified to produce ~6 μg of cDNA using Nugen WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies Inc, #3300-12).

treatment_protocol: Embryos frozen in OCT and sectioned at 10 microns. Laser microdissection of the lens placode on a Leica LMD-6000 system after slides were dipped in 70% ethanol at 4 °C for 1 min, washed in RNase-free water twice for 30 s, rinsed in 95% ethanol, and stained in Eosin Y. Stained samples were washed in 95% ethanol and dehydrated in 100% ethanol and xylene.

tag: strain/background

value: mixed (FVB; 129)

tag: genotype

value: surface ectoderm


title: WT1, E9.5

description:
7166151072_E
Total RNA amplified as cDNA.

source_name: WT lens placode

value: lens placode


title: CBP/p300 KO1, E9.5

description:
7166151072_B
Total RNA amplified as cDNA.


title: Wt_ liver_fasted_refed_3hr_ rep3

status: Public on Sep 23 2013

city: Providence

first: Joan

middle: M

last: Boylan

state: RI

address: 593 Eddy Street

department: Pediatrics

institute: Rhode Island Hospital

description: Gene expression data from liver taken from control adult mice fasted 16hr then given ad libitum access to food for 3 hr.

hyb_protocol: Following labeling, 3.1ug of cDNA were hybridized for17hr @ 45oC on a Genechip Mouse Gene 1.0ST array, then washed and stained according to the standard Affymetrix protocol.

scan_protocol: Genechips were scanned using a Affymetrix 3000 7G scanner

data_processing: Identification of differentially expressed genes was performed using the Partek Genomic Suite v 6.6beta.  CHP files were generated using Affymetrix Expression Console Software using default settings and the RMA algorithm.

source_name: liver,fasted,refed, 3hr

label_protocol: Biotinylated cDNA were prepared according to the WT Terminal Labeling and Hybridization for use with the Ambion WT Expression Kit Manual provided by Affymetrix using 100ng total RNA.

extract_protocol: RNA was extracted by the method of Chirgwin et al. Biochemistry18:5294-5299, 1979.

value: male

value: adult

value: liver

tag: treatment


title: RKO_liver_fasted_refed_3hr_rep4

description: Gene expression data from liver taken from adult mice with a liver specific knockout of RICTOR that were fasted 16hr then given ad libitum access to food for 3 hr.

value: Rictor floxed


title: RKO_liver_fasted_refed_3hr_rep2

value: fasted 16hr then given ad libitum access to food for 3 hr


title: Enterospheres_T3(100nm)_rep3

city: Tuebingen

first: Roland

middle: Alexander

last: Mohr

address: Oesterbergstrasse 3

department: Experimental Embryology

country: Germany

institute: Institute of Anatomy

description: Diff. enterospheres treated with T3 (100nm)

hyb_protocol: Standard Affymetrix hybridisation protocol

scan_protocol: Using Affymetrix GeneArray Scanner 3000 7G

data_processing: RMA normalisation using Partek 6.5 and the signals are log 2 transformed

source_name: enterospheres crafted from 3 neonatal C57BL/6 mice

label_protocol: Standard Affymetrix biotin labeling protocol

growth_protocol: For each sample, gut from 3 neonatal C57BL/6 mice (age up to 12 hours) were prepared. Circular muscle was removed, chopped and incubated in Collagenase Type XI (750 U/mL; Sigma-Aldrich, Taufkirchen, Germany) and Dispase II (250 µg/mL; Roche Diagnostics, Mannheim, Germany) dissolved in Hanks’ balanced salt solution with Ca2+/Mg2+ (HBSS; PAA, Pasching, Austria) for 30 min at 37 °C. Tissue was carefully trituated every 10 min with a flame polished blue pipette tip. Prior to the trituation, 0.05% DNAse I (Sigma-Aldrich) was added. After tissue dissociation, 10% fetal calf serum (FCS; PAA) was added. Remaining bigger cell constructs were removed by a 40 µm cell strainer. Two washing steps in HBSS were performed at 200 g, 23 °C. The pellet was resuspended in proliferation medium consistent of Dulbecco’s modified Eagle’s Medium with Ham’s F12 Medium (DMEM/F12; PAA) containing N2 supplement (1:100; Invitrogen GmbH, Darmstadt, Germany), a Penicillin/Streptomycin mix (1:100; PAA), L-Glutamine (1:100; PAA) and B27 serum free supplement (1:50; Invitrogen). Cells were seeded into 6-well plates (Becton-Dickinson, Franklin Lakes, NJ, USA) in a concentration of 2.5 x 10^4 cells / cm2. Epidermal growth factor (10 ng/mL; Sigma-Aldrich) and fibroblast growth factor (20 ng/mL; Sigma-Aldrich) were added every day. Cultures were incubated for 4 days at 37°C and 5 % CO2.

extract_protocol: Qiagen RNA protocol

treatment_protocol: After 4 days of proliferation, only free floating enterospheres were picked and transferred into petri dishes (Ø 60 mm, Greiner Bio One, Frickenhausen, Germany) in 5 ml fresh proliferation medium. Cell cultures were then incubated another 5 days with adding growth factors EGF / FGF daily. Then again, only free floating enterospheres (about 50 enterospheres / dish) were picked, washed 3 times in tris buffer and transferred into fresh petri dishes with differentiation medium (DMEM/F12 containing N2 supplement (1:100), Penicillin/Streptomycin (1:100), L-Glutamine (1:100) and ascorbic acid-2-phosphate (200 µmol/mL)). Incubation for another day followed, before 100 nm T3 was added to 50 % of the dishes. Remaining dishes served as controls. After 1 day incubation, enterospheres were picked, transferred into 1.5 ml Eppendorf cups and washed in tris buffer at 13k rpm for 10 min. Then, enterospheres were frozen in 300 µl RLT buffer / cup at -80 °C until RNA isolation.

tag: strain

value: enteric nervous system (ENS) tissue

value: neural progenitor cells (enterospheres)

value: 100 nm T3 for 1 day


title: WT3, E9.5

description:
7166151072_D
Total RNA amplified as cDNA.

value: wild type


title: Wt_ liver_fasted_refed_3hr_ rep1


title: Wt_ liver_fasted_refed_3hr_ rep4


title: Wt_ liver_fasted_refed_3hr_ rep2


title: Enterospheres_control_rep2

description: Diff. enterospheres untreated

value: untreated control


title: Enterospheres_T3(100nm)_rep2


title: RKO_liver_fasted_refed_3hr_rep1


title: DDLS8817 replicate 3

city: Cambridge

first: Martin

middle: L

last: Miller

address: Robinson Way

department: Cancer research UK, Cambridge Institute

institute: University of Cambridge

description: Replicate 3

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina Human HT-12 V3 Array. Slides were washed and stained in the Illumina instrument.

data_processing: BeadStudio version 3.3.7 Average Signal and Detection pvalue

source_name: Tumor resected from patient with DDLS

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

growth_protocol: DMEM medium, 10% FBS

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

treatment_protocol: No treatement was performed


title: LPS141 replicate 3

description: Replicate 3


title: LPS141 replicate 1

description: Replicate 1


title: Enterospheres_control_rep3

description: Diff. enterospheres untreated


title: DDLS8817 replicate 2

description: Replicate 2


title: LPS141 replicate 2

description: Replicate 2


title: DDLS8817 replicate 1

description: Replicate 1


title: Tumor-derived cell line DDLS8817

type: genomic

description: DNA copy number

hyb_protocol: Per manufacturer's instructions

scan_protocol: Per manufacturer's instructions

data_processing: Images quantified with Agilent Feature Extraction ver9.1. Probe sequences were re-mapped to the hg18 build of the human genome and merged. Probe-level data was subsequently normalized for local GC content with a two-stage LOESS fit. Probe-level data is the log2 ratio of cell-line-to-normal.

molecule: genomic DNA

source_name: cell line DNA

label_protocol: Bioprime Array CHG labeling kit (Invitrogen) using Cy3/Cy5

extract_protocol: Cells were lysed and genomic DNA extracted with the QIAGEN DNAeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: disease status

value: Dedifferentiated Liposarcoma

source_name: Promega reference DNA

tag: sample source

value: Promega reference DNA

value: normal


title: RKO_liver_fasted_refed_3hr_rep3


title: Tumor-derived cell line LPS141

description: DNA copy number


title: WT2, E9.5

description:
7166151072_A
Total RNA amplified as cDNA.


title: Liver_24hr_rapa_rep2

description: Gene expression data from liver taken from an adult mouse given an injection of 10mg/kg rapamycin for 24 hr.

hyb_protocol: Biotinylated cRNA was fragmented and hybridized at 45oC for 16hr according to Affymetrix directions.

scan_protocol: Chips were scanned on an Affymetrix 3000 scanner.

data_processing: The data were analyzed with Microarray Suite version 4.0 using Affymetrix default analysis settings.

source_name: liver, rapamycin, 24hr

label_protocol: Biotylated cRNA were prepared according to the Affymetrix protocol.

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's instructions

value: rapamycin, 24hr


title: Liver_24hr_vehicle_rep1

description: Gene expression data from liver taken from an adult mouse given an injection of 0.9% NaCL+2%ethanol for 24 hr.

source_name: liver, vehicle, 24hr

value: vehicle, 24hr


title: Liver_fasted_22hr+2hr_vehicle_refed_12hr_rep3

description: Gene expression data from liver taken from an adult mouse fasted 22hr then given an injection of 0.9% NaCL+2%ethanol for 2 hr followed by refeeding for 12hr.

source_name: liver, fasted 22hr, 2hr vehicle, refed 12hr

value: fasted 22hr, 2hr vehicle, refed 12hr


title: Liver_fasted_22hr+2hr_rapa_refed_12hr_rep1

description: Gene expression data from liver taken from an adult mouse fasted 22hr then given an injection of 10mg/kg rapamycin for 2 hr followed by refeeding for 12hr.

source_name: liver, fasted 22hr, 2hr rapamycin, refed 12hr

value: fasted 22hr, 2hr rapamycin, refed 12hr


title: Liver_fasted_22hr+2hr_rapa_refed_12hr_rep2

value: male


title: Liver_24hr_rapa_rep1

value: adult


title: Liver_24hr_vehicle_rep2

value: liver


title: Wild_type_Arabidopsis_3wk_seedling-rep1

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

description:
wt_rep1
Many seedlings were grown in one plate and several of them were harvested for RNA extraction

hyb_protocol: Hybridized using Gene Expression Hybridization kit (Agilent) and washed by Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).
Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction. After that, signal of each probe was divided by median value of filter-passed probes.

organism: Arabidopsis thaliana

label_protocol: 1 µg of total RNA was used for labeling procedure using QickAmp Labeling kit (One-color) (Agilent).

growth_protocol: All plants were grown in MS (1% sucrose) agar media in 16hr light / 8hr dark cycle in 23 Celsius degree.

extract_protocol: Plant RNeasy Mini kit (QIAGEN) was used to isolate total RNA.

tag: ecotype

value: wt

value: 3 weeks

value: whole seedlings


title: Liver_fasted_22hr+2hr_rapa_refed_12hr_rep3


title: Enterospheres_control_rep1

description: Diff. enterospheres untreated

value: enteric nervous system (ENS) tissue

value: neural progenitor cells (enterospheres)


title: CBP/p300 KO3, E10.5

description:
5550968027_C
Total RNA amplified as cDNA.

growth_protocol: Pregnant mice euthanized and embryos removed at E10.5.

value: mixed (FVB; 129)

value: surface ectoderm


title: Liver_fasted_22hr+2hr_rapa_refed_6hr_rep3

description: Gene expression data from liver taken from an adult mouse fasted 22hr then given an injection of 10mg/kg rapamycin for 2 hr followed by refeeding for 6hr.

source_name: liver, fasted 22hr, 2hr rapamycin, refed 6hr

value: fasted 22hr, 2hr rapamycin, refed 6hr


title: Liver_fasted_22hr+2hr_vehicle_refed_12hr_rep1


title: 35S:MYB106VP16_Arabidopsis_3wk_seedling-rep1

description:
MYB106VP16_rep1
Many seedlings were grown in one plate and several of them were harvested for RNA extraction


title: Wild_type_Arabidopsis_3wk_seedling-rep2

description:
wt_rep2
Many seedlings were grown in one plate and several of them were harvested for RNA extraction


title: Wild_type_Arabidopsis_3wk_seedling-rep3

description:
wt_rep3
Many seedlings were grown in one plate and several of them were harvested for RNA extraction


title: CBP/p300 KO1, E10.5

description:
5550968027_B
Total RNA amplified as cDNA.


title: 35S:MYB106VP16_Arabidopsis_3wk_seedling-rep4

description:
MYB106VP16_rep4
Many seedlings were grown in one plate and several of them were harvested for RNA extraction


title: Liver_fasted_22hr+2hr_vehicle_refed_12hr_rep2


title: 35S:MYB106VP16_Arabidopsis_3wk_seedling-rep2

description:
MYB106VP16_rep2
Many seedlings were grown in one plate and several of them were harvested for RNA extraction


title: Liver_fasted_22hr+2hr_rapa_refed_6hr_rep2


title: vector_control_Arabidopsis_2wk_seedling-rep4

description:
control_rep4
Many seedlings were grown in one plate and several of them were harvested for RNA extraction

value: wild type

value: 2 weeks


title: WT3, E10.5

description:
5550968027_A
Total RNA amplified as cDNA.

value: lens placode


title: WT2, E10.5

description:
5550968027_D
Total RNA amplified as cDNA.


title: Enterospheres_T3(100nm)_rep1

description: Diff. enterospheres treated with T3 (100nm)

value: 100 nm T3 for 1 day


title: Liver_fasted_22hr+2hr_rapa_refed_6hr_rep1


title: CBP/p300 KO2, E10.5

description:
5550968027_F
Total RNA amplified as cDNA.


title: WT1, E10.5

description:
5550968027_E
Total RNA amplified as cDNA.


title: Liver_fasted_22hr+2hr_vehicle_refed_6hr_rep2

description: Gene expression data from liver taken from an adult mouse fasted 22hr then given an injection of 0.9% NaCL+2%ethanol for 2 hr followed by refeeding for 6hr.

source_name: liver, fasted 22hr, 2hr vehicle, refed 6hr

value: fasted 22hr, 2hr vehicle, refed 6hr


title: Liver_fasted_22hr+2hr_rapa_refed_3hr_rep3

description: Gene expression data from liver taken from an adult mouse fasted 22hr then given an injection of 10mg/kg rapamycin for 2 hr followed by refeeding for 3hr.

source_name: liver, fasted 22hr, 2hr rapamycin, refed 3hr

value: fasted 22hr, 2hr rapamycin, refed 3hr


title: Liver_fasted_22hr+2hr_rapa_refed_3hr_rep2

value: male


title: Liver_fasted_22hr+2hr_rapa_refed_3hr_rep1

value: adult


title: 35S:MYB106VP16_Arabidopsis_3wk_seedling-rep3

description:
MYB106VP16_rep3
Many seedlings were grown in one plate and several of them were harvested for RNA extraction


title: Liver_fasted_22hr+2hr_vehicle_refed_3hr_rep3

description: Gene expression data from liver taken from an adult mouse fasted 22hr then given an injection of 0.9% NaCL+2%ethanol for 2 hr followed by refeeding for 3hr.

source_name: liver, fasted 22hr, 2hr vehicle, refed 3hr

value: liver

value: fasted 22hr, 2hr vehicle, refed 3hr


title: vector_control_Arabidopsis_2wk_seedling-rep2

description:
control_rep2
Many seedlings were grown in one plate and several of them were harvested for RNA extraction


title: Liver_fasted_22hr+2hr_rapa_rep3 (t=0)

description: Gene expression data from liver taken from an adult mouse fasted 22hr then given an injection of 10mg/kg rapamycin for 2 hr.

source_name: liver, fasted 22hr, 2hr rapamycin

value: fasted 22hr, 2hr rapamycin


title: Testis_T0_rep3

city: Rennes

first: Elisabeth

last: Sambroni

address: Bat 16A Campus de Beaulieu

department: PHASE

country: France

institute: INRA

hyb_protocol: Prehybridization of microarrays was performed in a hybridization buffer (5X Denhardt's, 5X SSC, 0.5% SDS) at 65°C for 4 hours. Labelled cDNA targets were denatured at 95°C for 5 minutes and incubated with microarrays for 48 hours at 65°C in the same buffer. Microarrays were then washed three times 1 hour at 68°C (0.1X SSC, 0.2% SDS).

scan_protocol: Microarrays were exposed 96 hours to phosphor-imaging plates that were scanned using a FUJI BAS 500 at 25 µm resolution. Signals acquisition was performed using the BZscan software.

data_processing: Raw expression signals were first corrected for the amount of spotted cDNA by dividing complex signals by oligonucleotide signals. To avoid the bias affecting relative gene expression levels, corrected sample signal of each spot was further multiplied by the median vector signal of all arrays for this same spot. Expression values (clones only) were then log2-transformed and submitted to a quantile-quantile normalisation using AMEN software (http://sourceforge.net/projects/amen/)

organism: Oncorhynchus mykiss

source_name: whole testis_T0_rep3

label_protocol: 5µg RNAs were reverse-transcribed for 2 hours at 42°C in presence of radiolabelled dNTP (30 µCi [alpha-33P] dCTP, 120 µM dCTP, 20 mM each dATP, dTTP, dGTP) using an oligo(dT) primer and 400 units Superscript II reverse transcriptase (Invitrogen).

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Cergy Pontoise, France). Total RNA concentration was determined on an Agilent 2100 Bioanalyzer and quality-controlled on a RNA 6000 LabChip® kit (Agilent Technologies, Stockport, UK).

treatment_protocol: Testes were collected from all-male population rainbow trout and chopped in small pieces, in sterile conditions. Fragments were randomly distributed on Nunc polycarbonate membrane inserts in 24-well plates filled with 300 µL of modified L15 culture medium plus 2% Ultroser SF. Incubation were performed in six replicates for 96 hours, at 12°C, in the absence or presence of purified trout Fsh alone (500 ng/mL) or combined to trilostane (10 µg/mL). A pre-incubation with trilostane was done for 1 hour before adding Fsh. Medium was replaced after 48 h of incubation.

value: Stage I-II

value: untreated

tag: time

value: 0 hour

value: whole testis (No culture)


title: Liver_fasted_22hr+2hr_vehicle_refed_3hr_rep1

tag: age


title: Liver_fasted_22hr+2hr_vehicle_refed_3hr_rep2


title: vector_control_Arabidopsis_2wk_seedling-rep1

description:
control_rep1
Many seedlings were grown in one plate and several of them were harvested for RNA extraction

value: whole seedlings


title: Testis_T0_rep2

source_name: whole testis_T0_rep2

value: Stage III


title: Liver_fasted_22hr+2hr_rapa_rep1 (t=0)

description: Gene expression data from liver taken froman adult mouse fasted 22hr then given an injection of 10mg/kg rapamycin for 2 hr.


title: vector_control_Arabidopsis_2wk_seedling-rep3

description:
control_rep3
Many seedlings were grown in one plate and several of them were harvested for RNA extraction

value: wild type


title: Liver_fasted_22hr+2hr_vehicle_refed_6hr_rep3


title: Liver_fasted_22hr+2hr_rapa_rep2 (t=0)


title: 35S:WIN1_Arabidopsis_2wk_seedling-rep1

description:
WIN1ox_rep1
Many seedlings were grown in one plate and several of them were harvested for RNA extraction

value: 2 weeks


title: Testis_T0_rep1

source_name: whole testis_T0_rep1


title: Liver_fasted_22hr+2hr_vehicle_rep3 (t=0)

description: Gene expression data from liver taken from an adult mouse fasted 22hr then given an injection of 0.9% NaCL+2%ethanol for 2 hr.

source_name: liver, fasted 22hr, 2hr vehicle

value: fasted 22hr, 2hr vehicle


title: 35S:WIN1_Arabidopsis_2wk_seedling-rep3

description:
WIN1ox_rep3
Many seedlings were grown in one plate and several of them were harvested for RNA extraction


title: wild_type_Arabidopsis_3wk_seedling-rep3

description:
wt_rep3
Many_seedlings were grown in one plate and several of them were harvested for RNA extraction

value: wt

value: 3 weeks


title: wild_type_Arabidopsis_3wk_seedling-rep4

description:
wt_rep4
Many_seedlings were grown in one plate and several of them were harvested for RNA extraction


title: wild_type_Arabidopsis_3wk_seedling-rep1

description:
wt_rep1
Many_seedlings were grown in one plate and several of them were harvested for RNA extraction


title: 35S:WIN1SRDX_Arabidopsis_3wk_seedling-rep4

description:
WIN1SRDX_rep4
Many_seedlings were grown in one plate and several of them were harvested for RNA extraction


title: wild_type_Arabidopsis_3wk_seedling-rep2

description:
wt_rep2
Many_seedlings were grown in one plate and several of them were harvested for RNA extraction


title: 35S:WIN1SRDX_Arabidopsis_3wk_seedling-rep3

description:
WIN1SRDX_rep3
Many_seedlings were grown in one plate and several of them were harvested for RNA extraction


title: Liver_fasted_22hr+2hr_vehicle_rep1_(t=0)


title: Liver_fasted_22hr+2hr_vehicle_rep2 (t=0)


title: Liver_fasted_24hr_rep1

description: Gene expression data from liver taken from an adult mouse fasted 24hr.

source_name: liver, fasted 24hr

value: fasted 24hr


title: Testis_Fsh+Tri_96h_rep3

description: Fsh +Tri 39

source_name: whole testis_Fsh+Tri_96h_rep3

value: Fsh 500 ng/mL combined with trilostane 10 µg/mL

value: 96 hours

value: whole testis (cultured)


title: CBP/p300 KO2, E9.5

description:
7166151072_F
Total RNA amplified as cDNA.

source_name: CBP/p300-/- surface ectoderm

value: mixed (FVB; 129)

value: surface ectoderm


title: Liver_fasted_24hr_rep5

value: male

value: adult

value: liver


title: Liver_fasted_24hr_rep3


title: Liver_fasted_24hr_rep2


title: Liver_fasted_24hr_rep4


title: Testis_Fsh+Tri_96h_rep4

description: Fsh +Tri 40

source_name: whole testis_Fsh+Tri_96h_rep4

value: Stage I-II


title: 35S:WIN1SRDX_Arabidopsis_3wk_seedling-rep1

description:
WIN1SRDX_rep1
Many_seedlings were grown in one plate and several of them were harvested for RNA extraction


title: Testis_Fsh+Tri_96h_rep5

description: Fsh +Tri 41

source_name: whole testis_Fsh+Tri_96h_rep5


title: Testis_Fsh+Tri_96h_rep2

description: Fsh +Tri 38

source_name: whole testis_Fsh+Tri_96h_rep2


title: Testis_Fsh+Tri_96h_rep6

description: Fsh +Tri 42

source_name: whole testis_Fsh+Tri_96h_rep6


title: 35S:MYB106SRDX_Arabidopsis_3wk_seedling-rep3

description:
MYB106SRDX_rep3
Many_seedlings were grown in one plate and several of them were harvested for RNA extraction


title: 35S:MYB106SRDX_Arabidopsis_3wk_seedling-rep2

description:
MYB106SRDX_rep2
Many_seedlings were grown in one plate and several of them were harvested for RNA extraction


title: 35S:MYB106SRDX_Arabidopsis_3wk_seedling-rep4

description:
MYB106SRDX_rep4
Many_seedlings were grown in one plate and several of them were harvested for RNA extraction


title: Testis_Tri_96h_rep5

description: Tri 29

source_name: whole testis_Tri_96h_rep5

value: Trilostane 10 µg/mL


title: Testis_Tri_96h_rep4

description: Tri 28

source_name: whole testis_Tri_96h_rep4


title: Testis_Tri_96h_rep6

description: Tri 30

source_name: whole testis_Tri_96h_rep6


title: 35S:WIN1SRDX_Arabidopsis_3wk_seedling-rep2

description:
WIN1SRDX_rep2
Many_seedlings were grown in one plate and several of them were harvested for RNA extraction


title: Testis_Fsh+Tri_96h_rep1

description: Fsh +Tri 37

source_name: whole testis_Fsh+Tri_96h_rep1

value: Stage III


title: 35S:MYB106SRDX_Arabidopsis_3wk_seedling-rep1

description:
MYB106SRDX_rep1
Many_seedlings were grown in one plate and several of them were harvested for RNA extraction


title: Testis_Tri_96h_rep1

description: Tri 25

source_name: whole testis_Tri_96h_rep1


title: Testis_Fsh_96h_rep6

description: Fsh 18

source_name: whole testis_Fsh_96h_rep6

value: Fsh 500 ng/mL


title: Testis_Tri_96h_rep3

description: Tri 27

source_name: whole testis_Tri_96h_rep3


title: Testis_Tri_96h_rep2

description: Tri 26

source_name: whole testis_Tri_96h_rep2


title: 016606

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
MG63 VV1 vs. MG63 SY1
Date:2006/11/29

hyb_protocol: CGH-Agilent-4rpm : 750.0 ng at 62 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : Kooperberg, Software used : rscript --> VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: MG63, VV1

label_protocol: Ambion protocol.

extract_protocol: Total RNA was extracted using TRIZOL reagent (Invitrogen). Cells were lysed in TRIZOL reagent solution, chloroform was added and the homogenate was centrifugated. One volume of 70% ethanol was added to the aqueous phase and the RNA were further purified on a silica-based membrane (RNeasy kit, Qiagen).

tag: cell type

value: osteosarcoma

tag: vector

value: control empty lentiviral vector

tag: label

value: MG63 VV1

tag: extract

tag: sample

tag: subject

tag: transduction

source_name: MG63, SY1

value: lentiviral vector encoding human syndecan-2

value: MG63 SY1


title: 016490

description:
U2OS SY2 vs. U2OS VV2
Date:2006/11/29

source_name: U2OS, SY2

tag: cell line

value: U2OS SY2

source_name: U2OS, VV2

value: U2OS VV2


title: GRX-overexpression seedlings, NaCl treatment, rep2

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

description: Gene expression data from NaCl-treated GRX overexpression Arabidopsis seedlings

hyb_protocol: Following fragmentation, 10 microgram of cRNA were hybridized for 16 h at 45 degree C on the rice Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChip were scanned using Affymetrix scanner

data_processing: CEL files wer imported into Genespring software and probe summarization and normalization was performed using RMA algorithm

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Wild-type and transgenic Arabidopsis seedlings were grown on MS medium for 14-days in a culture room with a daily photoperiodic cycle of 16h light and 8h dark

extract_protocol: Total RNA was extracted using TRI reagent according to the manufacturer's instructions

treatment_protocol: Seedlings were incubated in water (control) or 100 µM solution of indole-3-acetic acid (auxin, IAA), 200 mM sodium chloride (salt, NaCl) and 25 µM solution of methyl viologen (MV)for 3h

value: GRX-overexpression

tag: agent

value: NaCl

value: Columbia

tag: tissue

value: Seedlings

tag: Stage


title: 016609

description:
MG63 SY2 vs. MG63 VV2
Date:2006/11/29

source_name: MG63, SY2

value: MG63 SY2

source_name: MG63, VV2

value: MG63 VV2


title: GRX-overexpression seedlings, NaCl treatment, rep1

tag: genotype


title: GRX-overexpression seedlings, IAA treatment, rep2

description: Gene expression data from IAA-treated GRX overexpression Arabidopsis seedlings

value: IAA


title: Testis_Fsh_96h_rep2

description: Fsh 14

source_name: whole testis_Fsh_96h_rep2

tag: developmental stage

value: Stage I-II

tag: treatment

value: 96 hours

value: whole testis (cultured)


title: Wild-type seedlings, MV treatment, rep2

description: Gene expression data from MV-treated wild-type Arabidopsis seedlings

source_name: Wild-type seedlings, MV treatment, rep2

value: Wild-type

value: MV

tag: ecotype


title: Testis_Fsh_96h_rep3

description: Fsh 15

source_name: whole testis_Fsh_96h_rep3

value: Fsh 500 ng/mL

tag: time


title: Testis_Control_96h_rep6

description: Ctrl 6

source_name: whole testis_Control_96h_rep6

value: Control


title: Testis_Fsh_96h_rep1

description: Fsh 13

source_name: whole testis_Fsh_96h_rep1

value: Stage III


title: 016489

description:
U2OS VV1 vs. U2OS SY1
Date:2006/11/29

source_name: U2OS, VV1

value: osteosarcoma

value: control empty lentiviral vector

value: U2OS VV1

source_name: U2OS, SY1

value: lentiviral vector encoding human syndecan-2

value: U2OS SY1


title: Testis_Fsh_96h_rep4

description: Fsh 16

source_name: whole testis_Fsh_96h_rep4


title: Testis_Fsh_96h_rep5

description: Fsh 17

source_name: whole testis_Fsh_96h_rep5


title: SUM159 miR-203 rep3

city: Houston

first: Joe

last: Taube

state: Texas

address: 7435 Fannin St

department: Translational Molecular Pathology

institute: MD Anderson Cancer Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

value: pBabe puro miR-203

value: Claudin-low breast cancer


title: SUM159 Control rep3

value: control


title: SUM159 Control rep1


title: SUM159 miR-203 rep1


title: SUM159 miR-203 rep2


title: Testis_Control_96h_rep2

description: Ctrl 2

source_name: whole testis_Control_96h_rep2


title: Testis_Control_96h_rep5

description: Ctrl 5

source_name: whole testis_Control_96h_rep5


title: Testis_Control_96h_rep3

description: Ctrl 3

source_name: whole testis_Control_96h_rep3


title: Testis_Control_96h_rep4

description: Ctrl 4

source_name: whole testis_Control_96h_rep4


title: swedish subject, 1

city: Newark

first: Chuming

last: Chen

address: 15 Innovation Way, Suite 205

department: Computer and Information Sciences

institute: University of Delaware

data_processing: R/Bioconductor software was used to identify differentially expressed genes in the dataset. The Robust Multi-Array Average expression measure (RMA) was applied for background correction, quantile normalization, and output of gene expression values in log2 scale. We used the LIMMA package to assess differentially expressed genes, and statistical significance was adjusted for multiple testing by controlling the Benjamini and Hochberg’s false discovery rate at 5%.

source_name: vastus lateralis

label_protocol: 1-cycle target labeling at the NCI-Frederick Laboratory of Molecular Technology (http://ncifrederick.cancer.gov/atp/genetics-and-genomics/laboratory-of-molecular-technology/lmt-protocols-and-resources/)

growth_protocol: Vastus lateralis muscle biopsies were performed with a 6G Bergstrom needle. Muscle samples were frozen and stored in liquid nitrogen until RNA extraction.

extract_protocol: RNA from biopsies and cell pellets was prepared using the mirVana™ RNA Isolation Kit (Ambion). RNA quality was verified using an Agilent 2100 Bioanalyzer.

tag: sample designation/group

value: ISCU myopathy patient

tag: age at biopsy

tag: gender

value: F

tag: tissue type

value: vastus lateralis


title: Wild-type seedlings, IAA treatment, rep2

description: Gene expression data from IAA-treated wild-type Arabidopsis seedlings

value: IAA

value: Columbia

value: Seedlings


title: control, 4

value: healthy human control

value: M


title: control, 5


title: control, 3


title: SUM159 Control rep2


title: swedish subject, 3


title: swedish subject, 2


title: Xenopus embryo_morpholino injected_rep4

city: Pisa

first: Massimiliano

last: Andreazzoli

address: SS.12 Abetone e Brennero, 4

country: Italy

institute: University of Pisa

description: Labeled sample originates from total RNA pooled from 3 single embryos.

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 according to standard Affymetrix protocols.

data_processing: The data were normalized using the GC-RMA algorithm as implemented in the Bioconductor v. 2.9 software package. The data were analyzed using the MeV v. 4.8 software package.

label: Phycoerithrin

organism: Xenopus laevis

source_name: Xenopus early neurula, 1pM Morx1+400 pg GFP injected in both dorsal blastomeres at 4-cell stage, rep4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: After in vitro fertilization and collection. The embryos were cultured in Marc's Modified Ringer (MMR) solution at 0.1X dilution. After half an hour from fertilization, jelly coats were removed in a mildly reducing environment and then rinsed. Embryos were staged according to Nieuwkoop and Faber (Nieuwkoop and Faber, 1967).

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

treatment_protocol: For gain-of-function experiments, 50pg of wild-type Xrx1 mRNA were injected into both dorsal blastomeres of 4-cells stage embryos, using a Drummond ‘Nanoject’ apparatus. For loss-of-function experiments, 10pg of MoXrx1 morpholino antisense oligonucleotide were injeceted into both dorsal blastomeres at 4-cells stage embryos. Embryos were injected in 0.1X MMR and 4% Ficoll-400 (Sigma), and grown overnight at 14°C in the same solution. As experimental controls and for staging purposes, sibling uninjected embryos were grown in 0.1X MMR and 4% Ficoll-400 (Sigma) as well. Embryos for both experiments were collected at stage 13 but an aliquot was kept developing until stage 37/38, to assess final phenotype.

tag: protocol

value: whole embryo

value: Stage 13 (early neurula)


title: Xenopus embryo_morpholino injected_rep2

source_name: Xenopus early neurula, 1pM Morx1+400 pg GFP injected in both dorsal blastomeres at 4-cell stage, rep2


title: 35S:WIN1_Arabidopsis_2wk_seedling-rep2

description:
WIN1ox_rep2
Many seedlings were grown in one plate and several of them were harvested for RNA extraction

tag: age

value: 2 weeks

value: whole seedlings


title: control, 2


title: 08SE1891_Ulcerative colitis

city: London

first: Trinidad

last: Montero

address: Charterhouse Square

department: Biochemical Pharmacology

institute: Whilliam Harvey Research Institute, Bart's and The London School of Medicine; Queen Mary University of London

hyb_protocol: 15μg of each sample of cRNA was fragmented and used for hybridization on Human Genome U133 plus arrays (Affymetrix). After 16 hours of hybridization at 45ºC, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The images were scanned and analyzed with Affymetrix GeneChip Command Console (AGCC 1.1).

data_processing: The data were normalised using Bioconductor (RMA method).

source_name: Intestinal biopsy

label_protocol: Double-stranded cDNA (ds-cDNA) was synthesized from 2μg of total RNA using the One-Cycle cDNA Synthesis kit (Affymetrix) according to manufacturer´s protocol. In vitro transcription was performed with this ds-cDNA using the IVT Labelling kit (Affymetrix) and the cRNA obtained was purified with the GeneChip Sample Cleanup Module (Affymetrix).

extract_protocol: Total RNA was extracted using the RNeasy Micro kit (Qiagen).

tag: diagnosis

value: Ulcerative colitis

value: Female

tag: smoker

value: No


title: Testis_Control_96h_rep1

description: Ctrl 1

source_name: whole testis_Control_96h_rep1

value: Stage I-II

value: Control

value: 96 hours

value: whole testis (cultured)


title: Pax6 KO2, E10.25

description:
1957998056_D
Total RNA amplified to cDNA.

hyb_protocol: Performed using standard Illumina protocol on Illumina Mouse6 v1.1 bead arrays by the Genome Technology Access Center (GTAC) at Washington University.

data_processing:
Background subtraction and cubic spline normalization and differential expression performed using Illumina GenomeStudio software.
Mean hybridization intensity for all beads (25-50 per array) containing the indicated oligonucleotide probe.

source_name: Pax6-/- surface ectoderm

growth_protocol: Pregnant mice euthanized and embryos removed at E10.25.

extract_protocol: Total RNA was extracted and purified from the tissue obtained from one embryo using a Qiagen RNeasy Microkit (Qiagen# 74004). 15 ng of total RNA was amplified to produce 3-5 μg of cDNA using Nugen WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies Inc, #3300-12).

tag: strain/background

value: mixed (FVB; 129)

value: surface ectoderm


title: 08SE1913_Ulcerative colitis

value: Male


title: control, 1

value: F

value: vastus lateralis


title: Pax6 KO3, E10.25

description:
1957998056_F
Total RNA amplified to cDNA.


title: 08SE1890_Ulcerative colitis


title: Pax6 KO1, E10.25

description:
1957998056_B
Total RNA amplified to cDNA.


title: Xenopus embryo_morpholino injected_rep1

source_name: Xenopus early neurula, 1pM Morx1+400 pg GFP injected in both dorsal blastomeres at 4-cell stage, rep1


title: Xenopus embryo_morpholino injected_rep3

source_name: Xenopus early neurula, 1pM Morx1+400 pg GFP injected in both dorsal blastomeres at 4-cell stage, rep3


title: 08SE1888_Ulcerative colitis


title: WT3, E10.25

description:
1957998056_E
Total RNA amplified to cDNA.

source_name: WT lens placode

value: wild type

value: lens placode


title: 08SE1887_Ulcerative colitis


title: Xenopus embryo_control_rep6

source_name: Xenopus early neurula, uninjected embryo, rep6

value: uninjected

value: whole embryo

value: Stage 13 (early neurula)


title: 08SE1886_Ulcerative colitis

value: Ulcerative colitis


title: shRNA-mediated RUNX2 knockdown SKOV3 clone 3 vs control (mock-transfected) SKOV3 clone (dye-swap)

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

department: Medicine

institute: Laval university

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

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: shRNA-RUNX2 knockdown SKOV3 clone 3

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 µg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes.

growth_protocol: SKOV3 cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 (HyClone Europe Ltd, Cramlington, UK) supplemented with 10% heat-inactivated fetal calf serum, 2 mM l-glutamine, 1 mM sodium pyruvate, 100 units/ml penicillin and 100 μg/ml streptomycin (all reagents were from HyClone Europe). Cells were grown as adherent cells in a humidified atmosphere at 37°C in 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

treatment_protocol: The human ovarian adenocarcinoma SKOV3 cell line was stably transfected with RUNX2 shRNA cloned into the pLKO.1-puro vector. Viral supernatants were generated by transfecting 293T cells with the shRNA construct and the packaging vectors psPAX2 and pMD2.G (Addgene, Cambridge, MA). The high-titer lentiviral supernatants in the presence of 8 µg/ml polybrene were used to infect SKOV3 cells. Two days later, infected cells were treated with puromycin (0,5 µg/ml) for the selection of stably-transduced clones. The pLKO.1-puro vector encoding a scramble sequence not matching any mammalian sequence was used for the generation of mock-transduced (control) clones.

tag: cell type

value: ovarian adenocarcinoma  cell line

tag: cell line

source_name: control (mock-transfected) SKOV3 clone


title: WT1, E10.25

description:
1957998056_A
Total RNA amplified to cDNA.

tag: tissue


title: Xenopus embryo_control_rep10

source_name: Xenopus early neurula, uninjected embryo, rep10


title: Xenopus embryo_control_rep8

source_name: Xenopus early neurula, uninjected embryo, rep8


title: 35S:WIN1_Arabidopsis_2wk_seedling-rep4

description:
WIN1ox_rep4
Many seedlings were grown in one plate and several of them were harvested for RNA extraction

tag: genotype

value: 2 weeks

value: whole seedlings


title: shRNA-mediated RUNX2 knockdown SKOV3 clone 3 vs control (mock-transfected) SKOV3 clone


title: 08SE1885_Ulcerative colitis

value: No


title: Xenopus embryo_control_rep7

source_name: Xenopus early neurula, uninjected embryo, rep7

tag: developmental stage


title: Xenopus embryo_control_rep9

source_name: Xenopus early neurula, uninjected embryo, rep9


title: 08SE1882_Ulcerative colitis

value: Female


title: Differentiated 19BL induced pluripotent stem cell at Day11, biological rep2

city: Rochester

first: XING

last: LI

state: MN

address: 200 1st street SW

department: Health Sciences Research

institute: Mayo Clinic

description:
4F.d11.b
Differentiated 4F-iPSC at Day 11.
mRNA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with R/Bioconductor using RMA.

source_name: 19BL induced pluripotent stem cell, day11 differentiation

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

growth_protocol: Cells were grown onto mitomycin-inactivated feeders and cultured in mouse embryonic stem cell medium containing leukemia inhibitory factor (LIF).

extract_protocol: Qiagen RNeasy kit.

treatment_protocol: Pluripotent cells were spontaneously differentiated following an embryoid body (EB) formation protocol in differentiation medium with 20% FBS in the absence of LIF.

value: differentiated iPS cell line

tag: time point

value: day 11 of differentiation


title: Differentiated 19BL induced pluripotent stem cell at Day11, biological rep3

description:
4F.d11.c
Differentiated 4F-iPSC at Day 11.
mRNA


title: 08SE1884_Ulcerative colitis


title: Xenopus embryo_mRNA injected_rep5

source_name: Xenopus early neurula, 50pg Xrx1 mRNA+400 pg GFP injected in both dorsal blastomeres at 4-cell stage, rep5


title: 08SE1883_Ulcerative colitis


title: 08SE1881_Ulcerative colitis


title: 19BL induced pluripotent stem cell, biological rep3

description:
4F.c
4F-iPSC
mRNA

source_name: 19BL induced pluripotent stem cell, undifferentiated

value: iPS cell line

value: day 0 of differentiation


title: 08SE1878_Ulcerative colitis


title: Xenopus embryo_mRNA injected_rep3

source_name: Xenopus early neurula, 50pg Xrx1 mRNA+400 pg GFP injected in both dorsal blastomeres at 4-cell stage, rep3


title: Differentiated 19BL induced pluripotent stem cell at Day5, biological rep2

description:
4F.d5.b
Differentiated 4F-iPSC at Day 5.
mRNA

source_name: 19BL induced pluripotent stem cell, day5 differentiation

value: day 5 of differentiation


title: 08SE1879_Ulcerative colitis

source_name: Intestinal biopsy

value: Male


title: Differentiated 19BL induced pluripotent stem cell at Day5, biological rep3

description:
4F.d5.c
Differentiated 4F-iPSC at Day 5.
mRNA


title: Xenopus embryo_mRNA injected_rep2

source_name: Xenopus early neurula, 50pg Xrx1 mRNA+400 pg GFP injected in both dorsal blastomeres at 4-cell stage, rep2


title: Differentiated 19BL induced pluripotent stem cell at Day11, biological rep1

description:
4F.d11.a
Differentiated 4F-iPSC at Day 11.
mRNA


title: Xenopus embryo_mRNA injected_rep1

source_name: Xenopus early neurula, 50pg Xrx1 mRNA+400 pg GFP injected in both dorsal blastomeres at 4-cell stage, rep1


title: Liver_fasted_22hr+2hr_vehicle_refed_6hr_rep1

description: Gene expression data from liver taken from an adult mouse fasted 22hr then given an injection of 0.9% NaCL+2%ethanol for 2 hr followed by refeeding for 6hr.

source_name: liver, fasted 22hr, 2hr vehicle, refed 6hr

value: male

value: adult

value: liver

tag: treatment

value: fasted 22hr, 2hr vehicle, refed 6hr


title: Xenopus embryo_mRNA injected_rep4

source_name: Xenopus early neurula, 50pg Xrx1 mRNA+400 pg GFP injected in both dorsal blastomeres at 4-cell stage, rep4

value: whole embryo

value: Stage 13 (early neurula)


title: Differentiated 19BL induced pluripotent stem cell at Day5, biological rep1

description:
4F.d5.a
Differentiated 4F-iPSC at Day 5.
mRNA


title: 19BL induced pluripotent stem cell, biological rep2

description:
4F.b
4F-iPSC
mRNA


title: 19BL induced pluripotent stem cell, biological rep1

description:
4F.a
4F-iPSC
mRNA


title: Xenopus embryo_control_rep3

source_name: Xenopus early neurula, uninjected embryo, rep3

value: uninjected


title: Xenopus embryo_control_rep2

source_name: Xenopus early neurula, uninjected embryo, rep2


title: Xenopus embryo_control_rep5

source_name: Xenopus early neurula, uninjected embryo, rep5


title: 08SE1915_Crohn's Disease

value: Crohn's Disease


title: 08SE1880_Ulcerative colitis

value: Ulcerative colitis

value: Yes


title: Xenopus embryo_control_rep1

source_name: Xenopus early neurula, uninjected embryo, rep1


title: 08SE1914_Crohn's Disease

value: No


title: Xenopus embryo_control_rep4

source_name: Xenopus early neurula, uninjected embryo, rep4


title: Differentiated H9 induced pluripotent stem cell at Day11, biological rep2

description:
3F.d11.b
Differentiated 3F-iPSC at Day 11.
mRNA

source_name: H9 induced pluripotent stem cell, day11 differentiation

value: differentiated iPS cell line


title: 08SE1912_Crohn's Disease


title: Differentiated H9 induced pluripotent stem cell at Day11, biological rep1

description:
3F.d11.a
Differentiated 3F-iPSC at Day 11.
mRNA

value: day 11 of differentiation


title: Differentiated H9 induced pluripotent stem cell at Day5, biological rep3

description:
3F.d5.c
Differentiated 3F-iPSC at Day 5.
mRNA

source_name: H9 induced pluripotent stem cell, day5 differentiation


title: 08SE1901_Crohn's Disease

value: Female


title: Differentiated H9 induced pluripotent stem cell at Day5, biological rep2

description:
3F.d5.b
Differentiated 3F-iPSC at Day 5.
mRNA


title: 08SE1900_Crohn's Disease


title: Differentiated H9 induced pluripotent stem cell at Day11, biological rep3

description:
3F.d11.c
Differentiated 3F-iPSC at Day 11.
mRNA


title: 08SE1899_Crohn's Disease


title: Differentiated H9 induced pluripotent stem cell at Day5, biological rep1

description:
3F.d5.a
Differentiated 3F-iPSC at Day 5.
mRNA


title: Xenopus embryo_morpholino injected_rep5

description: Labeled sample originates from total RNA pooled from 3 single embryos.

source_name: Xenopus early neurula, 1pM Morx1+400 pg GFP injected in both dorsal blastomeres at 4-cell stage, rep5


title: H9 induced pluripotent stem cell, biological rep3

description:
3F.c
3F-iPSC
mRNA

source_name: H9 induced pluripotent stem cell, undifferentiated

value: iPS cell line

value: day 0 of differentiation


title: KO 4 wk Mat

city: San Francisco

first: Yuko

last: Oda

state: CA

address: 111N-MB 360 1700 Owens St, Suite 360

department: Endocrine Research

institute: VA Medical Center UCSF

description:
Incisors generate a few hairs internally
KO Mat

hyb_protocol: Standard Illumina hybridization protocol done by UCLA neuroscience genomics core

scan_protocol: Standard Illumina hybridication protocol done by UCLA neuroscience genomics core

data_processing: data were normalized by using quantile method in Genome studio (v.V2011.1; Module Gene Expression v.1.9.0).

source_name: MED1 KO_4wk_Mat

label_protocol: Standard Illumina hybridization protocol; cDNA is labeled by biotin and hybridized with Cy3-streptoavidin

growth_protocol: Coactivator MED1 is removed from keratin 14 (K14) expressing epithelia by using Crelox stragety

extract_protocol: Total RNA was isolated from dissected dental tissues by using Pico pure RNA purification kit (ABI)

treatment_protocol: Dental tissues generating hairs were dissected from MED1 KO mouse lower incisors, and the tissues from 3 mice were combined, then RNA extracted. Equivalent tissues in control littermate mice were also dissected.

tag: strain background

tag: genotype/variation

value: MED1 fl/fl K14 driven Cre

value: 4 weeks

tag: tissues

value: microdissected dental tissues from lower incisors

tag: Stage

value: Maturation Stage (Mat)


title: WT 4 wk Mat

description:
Incisors form enamel
WT Mat

source_name: Control (WT)_4wk_Mat

value: MED1 fl/fl


title: KO 4 wk Sec

description: KO Sec

source_name: MED1 KO_4wk_Sec

value: Secretion Stage (Sec)


title: 08SE1896_Crohn's Disease

source_name: Intestinal biopsy

tag: gender


title: H9 induced pluripotent stem cell, biological rep1

description:
3F.a
3F-iPSC
mRNA


title: 08SE1897_Crohn's Disease

value: Male


title: 08SE1894_Crohn's Disease


title: Control (WT) 4 wk CL

description: WT CL

source_name: Control (WT)_4wk_CL

value: Cervical Loop (CL)


title: Differentiated R1 embryonic stem cell at Day11, biological rep3

description:
R1.d11.c
Differentiated R1-ESC at Day 11.
mRNA

source_name: R1 embryonic stem cell, day11 differentiation

value: differentiated stem cell line


title: WT 4 wk Sec

description: WT Sec

source_name: Control (WT)_4wk_Sec


title: WT2, E10.25

description:
1957998056_C
Total RNA amplified to cDNA.

source_name: WT lens placode

label_protocol: The resulting cDNA was biotin labeled using the Illumina biotinylation kit.

value: mixed (FVB; 129)

value: wild type

value: lens placode


title: 08SE1889_Ulcerative colitis

value: Ulcerative colitis

value: No


title: Knockout (KO) 4 wk CL

description: KO CL

source_name: MED1 KO_4wk_CL


title: KO 10 wk Mat rep3

source_name: MED1 KO_10wk_maturation

value: 10 weeks

tag: phenotype

value: Incisors generate hairs but lack enamel

value: maturation stage (Mat)


title: 08SE1893_Crohn's Disease

value: Crohn's Disease

value: Female


title: KO 10 wk Mat rep4

value: MED1 fl/fl K14 driven Cre

tag: age

value: microdissected dental tissues from lower incisors


title: H9 induced pluripotent stem cell, biological rep2

description:
3F.b
3F-iPSC
mRNA

value: iPS cell line

value: day 0 of differentiation


title: 08SE1895_Crohn's Disease

tag: diagnosis

value: Male


title: KO 10wk Mat rep2


title: WT 10wk Mat rep 4

value: MED1 fl/fl

value: Incisors form enamel


title: 08SE1911_Healthy control

value: Healthy control

value: Unknown

tag: smoker


title: Knockout (KO) 10 wk Mat rep1


title: Differentiated R1 embryonic stem cell at Day5, biological rep3

description:
R1.d5.c
Differentiated R1-ESC at Day 5.
mRNA

source_name: R1 embryonic stem cell, day5 differentiation

value: differentiated stem cell line

value: day 5 of differentiation


title: Differentiated R1 embryonic stem cell at Day11, biological rep2

description:
R1.d11.b
Differentiated R1-ESC at Day 11.
mRNA

value: day 11 of differentiation


title: Differentiated R1 embryonic stem cell at Day5, biological rep2

description:
R1.d5.b
Differentiated R1-ESC at Day 5.
mRNA


title: 08SE1892_Crohn's Disease

value: Yes


title: 08SE1910_Healthy control


title: WT 10 wk Mat rep 3

value: 10 weeks


title: Differentiated R1 embryonic stem cell at Day11, biological rep1

description:
R1.d11.a
Differentiated R1-ESC at Day 11.
mRNA


title: R1 embryonic stem cell, biological rep2

description:
R1.b
R1-ESC
mRNA

source_name: R1 embryonic stem cell, undifferentiated

value: stem cell line


title: 08SE1904_Healthy control


title: 08SE1906_Healthy control


title: 08SE1898_Crohn's Disease

value: Crohn's Disease


title: 08SE1907_Healthy control


title: R1 embryonic stem cell, biological rep1

description:
R1.a
R1-ESC
mRNA


title: WT 10wk Mat rep2

value: maturation stage (Mat)


title: Control (WT) 10wk Mat rep1


title: Control (WT) 10wk CL

description: WT

value: Cervical loop (CL)


title: R1 embryonic stem cell, biological rep3

description:
R1.c
R1-ESC
mRNA


title: 08SE1903_Healthy control


title: Knockout (KO) 10wk CL

description: KO

source_name: MED1 KO_10wk_CL

value: MED1 fl/fl K14Cre

value: microdissected dental tissues from lower incisors


title: 08SE1905_Healthy control


title: Differentiated R1 embryonic stem cell at Day5, biological rep1

description:
R1.d5.a
Differentiated R1-ESC at Day 5.
mRNA


title: progerin 3

status: Public on Sep 22 2013

city: Chiba

first: Daisuke

last: Kinoshita

address: 1-8-1 Inohana, Chuo-ku

institute: Chiba University

description: gene expression of progerin over-expressing in p53-deficient VSMCs.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 026652_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: p53-deficient (E6-expressing) VSMCs infected with retroviral vector encoding progerin, line3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: VSMCs were purchased from Lonza, and cultured in smooth muscle basic medium (SmBM, Clonetics) supplemented with insulin, FGF-B, EGF, GA-1000, and FBS. The cultures were incubated at 37℃ in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated with RNA-Bee(Tel-Test, Inc). Cells were harvested 30 days after infected with lamin A or progerin.

treatment_protocol: p53-deficinet (E6-overexpressing) VSMCs were infected with retroviral vectors encoding lamin A or progerin.

value: vascular smooth muscle cells (VSMCs)

value: p53-deficient (E6-overexpressing)

tag: infected with retroviral vector to express

value: progerin


title: progerin 2

source_name: p53-deficient (E6-expressing) VSMCs infected with retroviral vector encoding progerin, line2

tag: cell type


title: progerin 4

source_name: p53-deficient (E6-expressing) VSMCs infected with retroviral vector encoding progerin, line4


title: progerin 1

source_name: p53-deficient (E6-expressing) VSMCs infected with retroviral vector encoding progerin, line1


title: BMDM_ProCyaA*_24h_rep1

city: Edinburgh

first: Nigel

last: Binns

address: The Chancellor's Building, 49 Little France Crescent

department: Division of Pathway Medicine

institute: The University of Edinburgh

description: bone marrow derived macrophages treated with ProCyaA* for 24hours.

hyb_protocol: Affymetrix 701027 rev 2: Hybridisation cocktails containing 15ug of biotinylated cRNA were constructed as defined in the Affymetrix GeneChip Expression analysis manual. All cocktails contained cRNA spikes from the Affymetrix GeneChip Eukaryotic hybridisation control kit. Labelled cRNAwas hybridised to the arrays overnight at 45 degrees C. Hybridised cRNA was then visualised by staining with streptavidin phycoerithrin

scan_protocol: GeneChip Scanner 3000:  The GeneChips were washed in a Gene- Chips Fluidics Station 400 (Affymetrix), and hybridisation visualised with a Gene Array Scanner2500 or 3000 using the Affymetrix software.

data_processing: Microarray suite 5 (MAS5) and Affymetrix GeneChips Operating Software 1.4 (GCOS1.4) were used to control analysis of Affymetrix GeneChips microarrays from experimental set up to data output. Additionally, much of the analysis of the Affymetrix arrays was performed using the Bioconductor 1.9 package running under the R2.4 environment. Empirical based statistical testing using Benjamini-Hochberg false discovery rate correction was used to determine significances between replicates and treatments (Po0.05 or Po0.01). In this report, genes that showed changes 43-fold were the focus of interest. A further criterion was created to select upregulated genes which were flagged as ‘‘present’’, as determined by MAS5, in all three replicates. GeneSpring 7.3.1 (Silicon Genetics, Redwood City, CA) was used to analyse the microarray data.

source_name: BMDM, ProCyaA*, 24hr

label_protocol: Affymetrix 701025 rev 2: 2ug Total RNA from each sample was used to prepare biotinylated target following the 'Eukaryotic Sample and Array Processing' - One-Cycle Target Labelling (1-15ug total RNA).

growth_protocol: Cells were grown in DMEM F-12 with Glutamax-1 and pyridoxine (Gibco) containing 10% heat-inactivated FCS (filtered) and pen-strep.

extract_protocol: Extraction of total RNA from BMDMs using Trizol reagent according to the manufacturer's instructions.

treatment_protocol: Cells were treated with 20ng/ml of the respective compound (diluted in media)

value: Bone marrow

value: Macrophage (BMDM)

tag: strain

value: Balb/C

value: male

value: ProCyaA*


title: BMDM_CyaA*_24h_rep1

description: bone marrow derived macrophages treated with CyaA* for 24hours.

source_name: BMDM, CyaA*, 24hr

tag: tissue

value: CyaA*


title: BMDM_Urea_24h_rep1

description: bone marrow derived macrophages treated with Urea for 24hours.

source_name: BMDM, Urea, 24hr

value: Urea


title: BMDM_CyaA_24h_rep1

description: bone marrow derived macrophages treated with CyaA for 24hours.

source_name: BMDM, CyaA, 24hr

value: 10 weeks

value: CyaA


title: BMDM_Urea_24h_rep3


title: BMDM_CyaA_24h_rep3


title: lamin A WT 2

description: gene expression of lamin A over-expressing in p53-deficient VSMCs.

source_name: p53-deficient (E6-expressing) VSMCs infected with retroviral vector encoding lamin A, line2

value: lamin A WT


title: lamin A WT 4

source_name: p53-deficient (E6-expressing) VSMCs infected with retroviral vector encoding lamin A, line4


title: lamin A WT 3

source_name: p53-deficient (E6-expressing) VSMCs infected with retroviral vector encoding lamin A, line3


title: lamin A WT 1

source_name: p53-deficient (E6-expressing) VSMCs infected with retroviral vector encoding lamin A, line1


title: BMDM_CyaA_24h_rep2


title: BMDM_Urea_24h_rep2


title: BMDM_ProCyaA*_24h_rep2


title: BMDM_ProCyaA*_24h_rep3


title: BMDM_CyaA*_24h_rep3


title: BMDM_CyaA*_24h_rep2


title: Multiple Sclerosis 4_2

status: Public on Sep 21 2013

city: Vienna

first: Isabella

last: Wimmer

address: Spitalgasse 4

department: Center for Brain Research

country: Austria

institute: Medical University of Vienna

description: Gene expression of initial lesion

hyb_protocol: The Hybridization Mix was prepared using the Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) and hybridized to the Arrays using the Agilent Microarray Hybridzation Chamber Kit (G2534A). After the hybridization, the Arrays were washed using the Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325) and Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326). The Hybridization was performed according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Protocol Version Feb.2007, Agilent Technologies)

scan_protocol: The scanning was done with the Agilent Microarray Scanner (Agilent p/n G2565BA). Information from scan data was processed using the Agilent’s Scan Control software, version A.7.0.1 and data were extracted with the Agilent Feature Extraction Software 9.5.1. The scanning as well as the feature extraction was performed according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Protocol Version Feb.2007, Agilent Technologies)

data_processing: The 75th percentile signal values were used to normalize the Agilent one-colour microarray signals. BEFORE 2013: Noramlization was done over all the cases included in each comparion (e.g. all 4 controls vs all 3 NAWMs)and log2fold changes were calculated with those normalized data. The log2fold change data matrix for each comparison [Control vs EL (=innate lesion), Control vs LL (=early demyelinated lesion), Control vs NAWM] is provided as a supplementary file on the Series records. Each file is a combination of the 7 Samples for each of the three comparisons described in the manuscript Fischer et al., 2012. UPDATE in 2013: Normalization was done over all 16 arrays.

source_name: Initial lesion

label_protocol: For the labeling, the Low RNA Input Linear Amplification Kit, PLUS, One colour was used (Agilent p/n 5188-5339). The labelled cRNA was purified using Quiagen’s RNeasy spin colums (RNeasy Mini Kit, Quiagen p/n 74104) and quantified using a NanoDrop ND-1000 Spectrophotometer. Labeling was performed according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Protocol Version Feb.2007, Agilent Technologies)

extract_protocol: Sections from formaldehyde-fixed, paraffin-embedded (FFPE) tissue were used. Consecutively cut sections of 6-10 µm were mounted on glass slides in RNAse-free conditions. The localization of interest was marked in the Klüver-Barrera stained slide which was used as template for the scratching with a scalpel from the unstained slices. The scratched FFPE material was collected, each region of interest to a separate Eppendorf tube. The scratched material in the Eppendorf tubes was deparaffinated with Xylol, afterwards total RNA was isolated using the Roche High Pure FFPE RNA Micro Kit. The mRNA in the isolate was then transcribed to the cDNA using the Paradise® Reagent System (Arcturus, USA). Two rounds of linear amplification were performed and the obtained purified aRNA was then sent to Imagenes (imaGenes GmbH, D-13125 Berlin, www.imagenes-bio.de) where the RNA was Cy 3 labeled and hybridized to human whole genome 4x44K Agilent platforms. The Roche High Pure FFPE RNA Micro Kit as well as the Paradise® Reagent System was used according to the instructions of the manufacturer.

tag: brain tissue

value: White matter

tag: disease state

value: initial lesion