title: rbf1120a biological rep2

city: Montreal

first: Heather

last: Collins

state: Quebec

address: 1205 Docteur Penfield Avenue

department: Biology

institute: McGill University

description: Gene expression data from rbf1120a eye discs

hyb_protocol: Hybridization was done according to standard Affymetrix procedures.  Hybridized cRNA was stained with streptavidin phycoerythrin.

scan_protocol: Scanning carried out using a Gene Array scanner according to standard Affymetrix procedures.

data_processing: Using Flexarray 1.1, data was adjusted, normalized and summarized using the RMA algorithm

organism: Drosophila melanogaster

source_name: Drosohila rbf1120a eye discs

label_protocol: RNA was reverse transcribed into cDNA and amplified using in vitro transcription to produce biotin-labeled cRNA

extract_protocol: RNA was extracted using miRNAeasy Mini Kit (Qiagen) according to the manufacturer's instructions.  Samples were treated using Rnase-free DNAse I (Qiagen).

value: eye discs

value: third instar larvae

value: rbf1120a Gal4


title: Aor_CT24

status: Public on Sep 30 2014

type: RNA

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

country: USA

institute: University of Pennsylvania

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Intensity values normalized using Affymetrix Expression Console software (GC-RMA).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: aorta

label_protocol: not provided

growth_protocol: C57/BL6 mice were entrained to a 12h light : 12h dark schedule for one week. Mice were then transferred to complete darkness prior to collection. Collection began at CT18. Mice were housed in light-tight boxes for the duration of the experiment.

extract_protocol: Organ samples were homogenized in Trizol reagent (Invitrogen) using a Tissuelyser (Qiagen). RNA was extracted using RNeasy columns (Qiagen) as per manufacturer’s protocol, then pooled from three mice for each organ and time point.

tag: strain

tag: tissue

value: aorta


title: TotalRNA_24h_0.5 nM 11-KT

city: Leipzig

first: Eva

last: Fetter

address: Permoserstraße 15

department: Bioanalytical Ecotoxicology

country: Germany

institute: UFZ-Helmholtz Centre for Environmental Research

description: Exposure with 11-ketotestosterone started at 96hpf

hyb_protocol: Hybridization was performed with Gene Expression Hybridization Kit (5188-5242) from Agilent according to the manufacturer instructions

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

organism: Danio rerio

source_name: Pool of 50 embryo_homogenate_24h_0.5 nM 11-KT

label_protocol: Labelling was performed with LowInput QuickAmp Kit One-Color (5190-2305) from Agilent according to the manufacturer instructions

growth_protocol: Embryos were kept in an incubator at 26°C with complete daily renewal of the embryonic media and a light cycle of 12:12 hours light:dark.

extract_protocol: Total RNA was isolated from 50 embryos using phase-lock tubes (5Prime GmbH, Hamburg) and Trizol (Invitrogen, Darmstadt) according to the manufacturer’s instructions. RNA was further purified using RNeasy Mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Zebrafish embryos were treated from 96 hpf to 120 hpf in a single experiment with three controls and 11 concentrations of 11-ketotestosterone ranging from 0.05-5000 nM.

tag: developmental stage

value: 120 hpf

value: OBI_established from local breader stock


title: rbf1120a biological rep3

country: Canada

tag: genotype


title: RLC_Heart_Male_78wks_Rep5

city: Jefferson

first: Vikrant

last: Vijay

state: AR

address: 3900 NCTR Road

department: Division of Systems Biology

institute: US FDA National Center for Toxicological Research

description: 78wks old untreated rats' total RNA was used for gene expression

hyb_protocol: Only the cRNAs with yields >1.65 µg and specific activities > 9.0 pmol of dye per µg cRNA were used for hybridization.  Labeled cRNAs were hybridized to microarray slides (4 arrays per slide) following the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (V5.5, Agilent Technologies, Inc.).

scan_protocol: The hybridized slides were scanned using a GenePix 4000B scanner (Axon Instruments, Sunnyvale, CA) at 5µm resolution using appropriate photomultiplier tube gain settings to obtain the highest intensity with <1% saturated pixels. The resulting images were analyzed by quantifying the Cy3 fluorescence intensity at each of the 45,018 gene spots (features) on each array using the Agilent Feature Extraction Software (V9.5).  The median fluorescence intensity of all the pixels within each feature was taken as the intensity value for that feature.

data_processing: A total of 30 raw data files for 30 arrays (samples) (5 arrays for each sex at 3 ages) were obtained from the Agilent Feature Extraction Software (Agilent Technologies, Inc.). An excel spreadsheet containing  raw intensity data  for all 30 samples was used as an input file for further data preprocessing and normalization using SAS 9.1.3 (SAS institute Inc., Cary, NC).  There were 45,018 features (probes) on each array with gene annotations available for 28,552 probes (18,157 unique genes with variable number of probes per gene) (Kwekel et al., 2013). Average probe intensity was calculated for each gene, then non-expressed genes were removed and data was normalized using 75th percentile scaling.

organism: Rattus norvegicus

source_name: Whole Heart, male, 78wks, untreated, replicate 5

label_protocol: Total RNAs (500ng) were labeled with cyanine dye (Cy3-CTP) using the Agilent One Color Low RNA Input Linear Amplification Kit according to the manufacturer’s protocol (Agilent Technologies, Inc.). For each reaction, cRNA yields and specific activities were determined using the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Male and female Fischer 344 (F344) rats obtained from the National Center for Toxicological Research (NCTR) breeding colony were fed NIH-31 diet and water ad libitum and housed under AAALAC (Association for Assessment and Accreditation of Laboratory Animal Care) approved conditions of 12/12-hr light/dark cycle, and were maintained at 23 °C with a relative humidity of 50%.

extract_protocol: Total RNAs were extracted from heart tissue powder using the Qiagen RNeasy mini kit (Qiagen Inc., Valencia, CA) with some modifications. In brief, heart tissue powder was homogenized using the FastPrep homogenizer (Qbiogene, Inc., Carlsbad, CA) for 2 x 40 seconds in RLT buffer (Qiagen, Inc.). The homogenate was centrifuged at 4000 x g for 5 min. To the resultant supernatant, an equal volume of ethanol was added followed by vigorous shaking. The samples were immediately applied to an RNeasy mini column (Qiagen, Inc.) and centrifuged at 4000 x g for 10 min. This was followed by on-column treatment with DNase I to remove any residual DNA from the RNA samples before final elution. The purity and yield of each RNA sample were determined using the NanoDrop ND-1000 Spectrophotometer (Thermo Scientific, Wilmington, DE). The ratios of A260/280 from all the RNA samples ranged from 1.8 to 2.0. The quality of the extracted RNAs was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).  RNA samples with RNA Integrity Numbers (RINs) of 8.0 or above were used for gene expression measurements.

treatment_protocol: No treatments

value: Fischer 344

value: Heart

tag: gender

value: Male

tag: age


title: Liver_PXR KO_Vehicle_Rep1

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Normalized expression of probe level data was calculated using the Robust Multiarray Average function (RMA) implemented in Bioconductor's affy-package

label: Biotin

source_name: Liver_PXR KO_Vehicle

label_protocol: Standard Affymetrix procedures

growth_protocol: Adult male wild-type mice and PXR-KO mice were maintained on standard laboratory chow and were allowed food and water ad libitum.

extract_protocol: Total RNA was extracted and transcribed to cDNA

treatment_protocol: Portions of the livers were rapidly snap-frozen in liquid nitrogen and stored at -70°C until analysis.

value: Pxr knockout

tag: Sex

value: Liver

tag: compound

value: Vehicle

tag: route

value: IP

tag: dose

value: 0 mg/kg


title: rbf1120a biological rep1


title: RLC_Heart_Male_78wks_Rep4

source_name: Whole Heart, male, 78wks, untreated, replicate 4


title: TotalRNA_24h_Control_2

source_name: Pool of 50 embryo_homogenate_24h_Control_2


title: TotalRNA_24h_0.05 nM 11-KT

source_name: Pool of 50 embryo_homogenate_24h_0.05 nM 11-KT


title: RLC_Heart_Male_78wks_Rep2

source_name: Whole Heart, male, 78wks, untreated, replicate 2


title: RLC_Heart_Male_78wks_Rep3

source_name: Whole Heart, male, 78wks, untreated, replicate 3


title: Aor_CT20


title: RLC_Heart_Male_78wks_Rep1

source_name: Whole Heart, male, 78wks, untreated, replicate 1


title: w1118 psc overexp biological rep3

description: Gene expression data from w1118 psc eye discs

source_name: Drosophila control eye discs overexpressing PSC

value: w1118 psc


title: w1118 psc overexp biological rep2


title: TotalRNA_24h_Control_1

source_name: Pool of 50 embryo_homogenate_24h_Control_1


title: w1118 psc overexp biological rep1


title: Aor_CT18


title: TotalRNA_24h_Control_3

source_name: Pool of 50 embryo_homogenate_24h_Control_3


title: w1118 biological rep3

description: Gene expression data from w1118 eye discs

source_name: Drosophila control eye discs


title: RLC_Heart_Female_78wks_Rep5

source_name: Whole Heart, female, 78wks, untreated, replicate 5

value: Female


title: Adr_CT64

source_name: adrenal gland

value: adrenal gland


title: Adr_CT62


title: RLC_Heart_Female_78wks_Rep4

source_name: Whole Heart, female, 78wks, untreated, replicate 4


title: w1118 biological rep2

value: eye discs


title: Aor_CT22

source_name: aorta


title: RLC_Heart_Female_78wks_Rep3

source_name: Whole Heart, female, 78wks, untreated, replicate 3


title: w1118 biological rep1

value: third instar larvae


title: Adr_CT60


title: Adr_CT58


title: T8-without NaCl-log phase-rep2

city: TOULOUSE

first: CEREN

last: ALKIM

address: Laboratoire d'Ingénierie des Systèmes Biologiques & des Procédés

country: France

institute: INRA

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast V2 Oligo Microarrays (G4813A-016322) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, 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: 016322_D_F_20070321).  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Saccharomyces cerevisiae CEN.PK113-7D

source_name: NaCl-resistant Saccharomyces cerevisiae, log. Phase, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.5 µg RNA using the One-color Low Input Quick Amp Kit (Agilent) according to the manufacturer's instructions, followed by Agilent Nano-prep RNA purification (Agilent, Santa Clara, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-2000 spectrophotometer.

growth_protocol: Fresh precultures of yeast cells were diluted to an OD600 of 0.1 in fresh minimal medium. They were cultivated at 30°C and 150 rpm untill they reach the OD600 value of about 1.00. Cells were harvested at this OD600 value.

extract_protocol: Total RNA of yeast cells were extracted by using RNeasy Mini Kit supplied from QIAGEN according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Yeast cells were not treated with any special agent.

tag: mating type

value: MATa

tag: genotype/variation

value: NaCl-resistant mutant


title: Wild Type-without NaCl-log phase-rep3

source_name: Saccharomyces cerevisiae, log. Phase, replicate 3

value: wild type


title: 2_02_shHIF1b_EBd6

city: Los Angeles

first: William

last: Lowry

state: CA

address: 621 Charles Young Drive South

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Embryoid bodies generated fromhESC HSF1 shHIF1β line cultured in 2% oxygen for 6 days after EB induction

hyb_protocol: Labeled cRNA was mixed with hybridization mix according to Affymetrix protocol and hybridized in Affymetrix GeneChip hybridization oven 645 at 45C for 16 hours with rotation at 60 rpm.

scan_protocol: Scanning was performed on Affymetrix 7G scanner with target intensity 500

data_processing: Cel files were imported into Genespring and RMA normalized.

organism: Homo sapiens

label_protocol: Labeling was performed with Ambion MESSAGEAMP PREMIER kit (cat#: 4383452)

growth_protocol: Atmospheric oxygen tension growth was established in 20% O2, 5% CO2, and 75% N2. Neural progenitor cells were generated by growing pluripotent stem cells for at least 7 days in DMEM/F12 with N2 and B27 supplements, 20 ng/mL basic fibroblast growth factor (FGF), 1µM retinoic acid, and 1µM Sonic Hedgehog Agonist (SAG) to form rosettes. Once rosettes were picked, they were then cultured in NPC medium containing DMEM/F12, N2 and B27, 20 ng/ml basic FGF, and 500ng/ml epidermal growth factor (EGF). To generate embryoid bodies, embryonic stem cell colonies were dissociated from the plate mechanically and cultured in ultra-low attachment plates containing DMEM/F12 supplemented with 20% knockout serum replacement media, L-glutamine, nonessential amino acids, and penicillin–streptomycin.

extract_protocol: RNA extracted using Qiagen RNeasy mini Kit with DNAse digestion according to the manufacturer's instructions.

treatment_protocol: Physiological oxygen tension growth was established in 2% O2, 5% CO2, and 92% N2. Deferoxamine (DFX) (Sigma) was added at the NPC medium for 5 days, and the concentration (100 to 200µM) was adjusted for each cell line individually.

tag: cell type

value: Embryoid bodies generated from hESC HSF1


title: T8-without NaCl-log phase-rep1

source_name: NaCl-resistant Saccharomyces cerevisiae, log. Phase, replicate 1


title: Wild Type-without NaCl-log phase-rep2

source_name: Saccharomyces cerevisiae, log. Phase, replicate 2


title: RLC_Heart_Female_78wks_Rep2

source_name: Whole Heart, female, 78wks, untreated, replicate 2

value: Fischer 344


title: 2_02_shHIF1b_ES

description: hESC HSF1 shHIF1β cell line cultured in 2% oxygen for 5 days

value: hESC HSF1


title: Wild Type-without NaCl-log phase-rep1

source_name: Saccharomyces cerevisiae, log. Phase, replicate 1


title: RLC_Heart_Male_21wks_Rep4

description: 21wks old untreated rats' total RNA was used for gene expression

source_name: Whole Heart, male, 21wks, untreated, replicate 4

value: Heart

value: Male


title: RLC_Heart_Male_21wks_Rep3

source_name: Whole Heart, male, 21wks, untreated, replicate 3


title: RLC_Heart_Female_78wks_Rep1

source_name: Whole Heart, female, 78wks, untreated, replicate 1


title: Adr_CT56


title: RLC_Heart_Male_21wks_Rep5

source_name: Whole Heart, male, 21wks, untreated, replicate 5


title: 20_O2_ctrl_EBd6

description: Embryoid bodies generated from hESC HSF1 scramble control line cultured in 20% oxygen for 6 days


title: Adr_CT52


title: Adr_CT50


title: Adr_CT54


title: 2_02_ctrl_EBd6

description: Embryoid bodies generated from hESC HSF1 scramble control line cultured in 2% oxygen 6 days after EB induction


title: 2_02_ctrl_ES

description: hESC HSF1 scramble control cell cultured in 2% oxygen for 5 days


title: RLC_Heart_Male_21wks_Rep2

source_name: Whole Heart, male, 21wks, untreated, replicate 2


title: 20_O2_ctrl_ES

description: hESC HSF1 scramble control cell cultured in 20% oxygen


title: RLC_Heart_Male_21wks_Rep1

source_name: Whole Heart, male, 21wks, untreated, replicate 1


title: XFiPS_NPC_DFX

description: NPCs derived from XFiPS-line treated with DFX for 5 days

value: NPCs derived from XFiPS-line


title: XFiPS_NPC_ctrl

description: NPCs derived from XFiPS-line without DFX


title: Adr_CT48


title: LN229-SOX4

city: hangzhou

first: jie

last: liu

address: yuhangtang road 866

country: China

institute: zcni

description: SOX4 overexpression LN229

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hours at 45 ℃ onPrimeView Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix fluidics Station 450.

scan_protocol: The chips were scanned with the affymetrix genechip 7G plus, and AGCC is used for the image processing

data_processing: Expression Console is used for normalizing the chip data and analyzing the fold change

source_name: LN229_SOX4 overexpression

label_protocol: Start with 250ng total RNA, and Biotinylated cRNA were prepared according to the standard Affymetrix protocol, in which, GeneChip 3 IVT Express Kit (Lot no.901228) is used in the experiment.

growth_protocol: cells were cultured in DMEM with 10% FBS

extract_protocol: total RNA was extracted with Trizol according to the manufacturer's protocol

treatment_protocol: SOX4 was overexpressed with pBrit-Flag-SOX4-HA or pBrit-Flag-HA in LN229

tag: cell line

value: glioblastoma cells

tag: expressing

value: SOX4 overexpression


title: RLC_Heart_Female_21wks_Rep5

source_name: Whole Heart, female, 21wks, untreated, replicate 5


title: RLC_Heart_Female_21wks_Rep3

source_name: Whole Heart, female, 21wks, untreated, replicate 3


title: Adr_CT42

source_name: adrenal gland


title: 2_02_NPC_scramble

description: NPCs cultured in 2% oxygen derived from HSF1 scramble control human ES line

value: NPCs derived from HSF1 human ES line


title: Adr_CT44


title: PSC_NPC_DFX

description: NPCs derived from human ES line treated with DFX for 5 days

value: NPCs derived from human ES line


title: LN229-control

description: LN229 control

value: pBrit-Flag-HA

value: control


title: 2_02_NPC_shHIF1b

description: NPCs cultured in 2% oxygen derived from HSF1 human ES line with stable knockdown of HIF1β


title: HSF1_NPC_DFX

description: NPCs derived from HSF1 human ES line treated with DFX for 5 days


title: Adr_CT40

value: adrenal gland


title: Adr_CT38


title: PSC_NPC_ctrl

description: NPCs derived from human ES line without DFX


title: RLC_Heart_Female_21wks_Rep2

source_name: Whole Heart, female, 21wks, untreated, replicate 2

value: Female


title: RLC_Heart_Male_8wks_Rep5

description: 8wks old untreated rats' total RNA was used for gene expression

source_name: Whole Heart, male, 8wks, untreated, replicate 5


title: HSF1_NPC_ctrl

description: NPCs derived from HSF1 human ES line without DFX


title: Adr_CT32


title: RLC_Heart_Female_21wks_Rep1

source_name: Whole Heart, female, 21wks, untreated, replicate 1


title: Adr_CT36


title: Adr_CT34


title: RLC_Heart_Male_8wks_Rep2

source_name: Whole Heart, male, 8wks, untreated, replicate 2


title: T8-without NaCl-log phase-rep3

source_name: NaCl-resistant Saccharomyces cerevisiae, log. Phase, replicate 3

value: MATa


title: Adr_CT30


title: RLC_Heart_Male_8wks_Rep1

source_name: Whole Heart, male, 8wks, untreated, replicate 1


title: RLC_Heart_Male_8wks_Rep3

source_name: Whole Heart, male, 8wks, untreated, replicate 3


title: RLC_Heart_Male_8wks_Rep4

source_name: Whole Heart, male, 8wks, untreated, replicate 4


title: Genomic DNA from mature dendritic cells_12

type: genomic

city: Davis

first: Hong

last: Ji

address: County Rd 98 & Hutchison Drive

institute: University of California Davis

description:
Sample 12
mature dendritic cell generated ex vivo using Jonuleit cocktail

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

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

data_processing:
BeadStudio software v1.2
GSGX Version: 1.1.0
Report Date: 7/25/14 13:03
Project: Hong450_illuminaNormBgrd
Group Set: new
Analysis: hong450_illuminaNormBgrd
Normalization: controls

label: Cy5 and Cy3

molecule: genomic DNA

source_name: mature dendritic cell

label_protocol: Standard Illumina Protocol

growth_protocol: Monocytes were cultured in the presence of GM-CSF (1000U/ml) and IL-4 (500U/ml) for 4 days to induce differentiation into mostly immature monocyte-derived DCs. These DCs were matured by culturing for an additional two days in the presence of Jonuleit cocktail (IL1β, IL1α, IL6, TNFα and PGE2)

extract_protocol: Genomic DNA was extracted using Qiagen Allprep micro kit according to manufacturer’s  instructions.

tag: ID

value: mature dendritic cell


title: Genomic DNA from mature dendritic cells_11

description:
Sample 11
mature dendritic cell generated ex vivo using Jonuleit cocktail


title: Genomic DNA from mature dendritic cells_10

description:
Sample 10
mature dendritic cell generated ex vivo using Jonuleit cocktail


title: Adr_CT26


title: Adr_CT24


title: Adr_CT28


title: RLC_Heart_Female_8wks_Rep5

source_name: Whole Heart, female, 8wks, untreated, replicate 5


title: Genomic DNA from mature dendritic cells_9

description:
Sample 9
mature dendritic cell generated ex vivo using Jonuleit cocktail


title: Non responder_PAC6_CardA

city: Pamplona

first: Alfonso

last: Calvo

state: Navarra

address: Pio XII, 55

department: Oncology

country: Spain

institute: CIMA

data_processing:
The normalization and all the data analysis were performed with R2.15 Bioconductor 2.10
For the normalization it was used the platform normalizer MammU6.
Fold_Change.txt reports ΔΔCt for each statitistical contrast (ΔΔCt = test deltaCt - reference deltaCt).

label: FAM

source_name: MRCC patient_sunitinib_non-responder

label_protocol: 350ng of total RNA from each patient was first reverse-transcribed using a stem-loop RT Megaplex Primer Pool and the Taqman MicroRNA Reverse Transcription Kit (Applied Biosystem). cDNAs were preamplified with the TaqMan Preamp Master Mix kit and Megaplex Preamp Primer Human pools. Expression of 667 human mature miRNAs and 6 endogenous controls was profiled using TLDA microfluidic cards A and B (Applied Biosystem) on a 7900HT Fast real time system.

extract_protocol: Total RNA was extracted with the RecoverAllTM Total Nucleic Acid Isolation Kit (Ambion).

treatment_protocol: Tumor confirmed by pathologist tissues samples were formalin-fixed and paraffin-embedded (FFPE). Blocks were sliced into 10µm sections.

tag: disease

value: metastatic renal-cell carcinoma (MRCC)

tag: response to sunitinib treatment

value: non-responder (resistant)

tag: patient status

value: Patient with clear cancer progression after sunitinib treatment

value: 4 unstained sections of FFPE tumor tissue from MRCC patient before treatment


title: HUF88P4, vehicle + NOTCH1 shRNA

city: Guangzhou

first: Ren-Wei

last: Su

state: Guangdong

address: 483 Wushan Road

department: Histology and Embryology

institute: South China Agricultural University

description: Gene expression data from HUF88P4 without EPC treatment, transfected with NOTCH1 shRNA plasmid

hyb_protocol: Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization. Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400

scan_protocol: Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Raw data were processed using Affymetrix GCOS version 1.4

label_protocol: Approximately 1 micrograms of total RNA was processed to produce biotinylated cRNA targets using the older (ENZO) Affymetrix protocol

growth_protocol: HuF cells were cultured in phenol-red-free RPMI 1640, with 10% charcoal-dextran stripped fetal bovine serum (CDS-FBS), 0.1mM sodium pyruvate, and 1x Pen/Strep/Fungizone (all from Gibco, Gaithersburg, MD) in an incubator at 37oC, 5% CO2.

extract_protocol: All RNA samples were isolated using the RNeasy kit from QIAGEN (Valencia, CA).

treatment_protocol: HuF cells were cultured in 60mm dish with 3 ml of growth media until approximately 60% confluence, 1 ml of 293FT cell lysate containing the virus was then added for transfection and media was changed back to growth media 24 hours after the addition of the virus. At approximately 80% confluence, the cell culture medium for HuF cells or primary stromal cells was changed to RPMI 1640 supplemented with 2% CDS-FBS, sodium pyruvate, penicillin/streptomycin. After the 24-h pre-culture, cells were untreated or treated with EPC cocktail [36 nM estradiol-17β and 1 μM medroxyprogesterone acetate (MPA)], and 0.1 mM dbcAMP (Sigma, St. Louis, MO)] for 6-8 days, with medium change every three days.

tag: decidualization

value: No

tag: shRNA

value: NOTCH1 shRNA


title: Genomic DNA from immature dendritic cells_5

description:
Sample 5
immature dendritic cell generated ex vivo from monocye

source_name: immature dendritic cell

value: immature dendritic cell


title: HUF88P4, EPC + NOTCH1 shRNA

description: Gene expression data from HUF88P4 with EPC treatment, transfected with NOTCH1 shRNA plasmid

value: Yes


title: HUF88P4, EPC + control shRNA

description: Gene expression data from HUF88P4 with EPC treatment, transfected with control shRNA plasmid

value: control shRNA


title: Non responder_PAC5_CardA

tag: tissue


title: Genomic DNA from immature dendritic cells_6

description:
Sample 6
immature dendritic cell generated ex vivo from monocye


title: HUF86P4, EPC + NOTCH1 shRNA

description: Gene expression data from HUF86P4 with EPC treatment, transfected with NOTCH1 shRNA plasmid


title: HUF86P4, EPC + control shRNA

description: Gene expression data from HUF86P4 with EPC treatment, transfected with control shRNA plasmid


title: RLC_Heart_Female_21wks_Rep4

description: 21wks old untreated rats' total RNA was used for gene expression

source_name: Whole Heart, female, 21wks, untreated, replicate 4

tag: strain

value: Fischer 344

value: Heart

tag: gender

tag: age


title: Genomic DNA from immature dendritic cells_8

description:
Sample 8
immature dendritic cell generated ex vivo from monocye


title: Non responder_PAC2_CardA


title: Adr_CT22


title: Genomic DNA from monocyte_4

description:
Sample 4
monocyte isolated from human blood

source_name: monocye

value: monocye


title: Genomic DNA from immature dendritic cells_7

description:
Sample 7
immature dendritic cell generated ex vivo from monocye


title: Adr_CT20


title: Responder_PAC4_CardA

source_name: MRCC patient_sunitinib_responder

value: responder (sensitive)

value: Patient with clinical benefit after sunitinib treatment


title: Responder_PAC3_CardA


title: Adr_CT18

value: adrenal gland


title: RLC_Heart_Female_8wks_Rep2

description: 8wks old untreated rats' total RNA was used for gene expression

source_name: Whole Heart, female, 8wks, untreated, replicate 2

value: Female


title: RLC_Heart_Female_8wks_Rep3

source_name: Whole Heart, female, 8wks, untreated, replicate 3


title: RLC_Heart_Female_8wks_Rep4

source_name: Whole Heart, female, 8wks, untreated, replicate 4


title: Genomic DNA from monocyte_3

description:
Sample 3
monocyte isolated from human blood


title: Responder_PAC1_CardA


title: HUF88P4, vehicle + control shRNA

description: Gene expression data from HUF88P4 without EPC treatment, transfected with control shRNA plasmid


title: HUF86P4, vehicle + control shRNA

description: Gene expression data from HUF86P4 without EPC treatment, transfected with control shRNA plasmid


title: Adr_CT46

source_name: adrenal gland


title: Genomic DNA from monocyte_1

description:
Sample 1
monocyte isolated from human blood


title: RLC_Heart_Female_8wks_Rep1

source_name: Whole Heart, female, 8wks, untreated, replicate 1


title: Goserelin, Subject-D

city: Copenhagen

first: Peter

last: Schjerling

address: Bispebjerg Bakke 23, M81

department: Institute of Sports Medicine Copenhagen, ISMC

country: Denmark

institute: Bispebjerg Hospital

hyb_protocol: After fragmentation at 94°C for 35 min in fragmentation buffer (40 mM Tris, 30 mM magnesium acetate, 10 mM potassium acetate), the labelled cRNA was hybridized for 16 h to Affymetrix HG-U133 Plus 2.0 (Affymetrix, Santa Clara, CA, USA).  After hybridization the array was washed and stained with streptavidin phycoerythrin solution using the Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The probe data (CEL files) were analyzed with the Partek Genomic Suite v6.6 (Partek, MO, USA) using the RMA normalization method.

source_name: Vastus lateralis muscle 4 hours after last strength training session, goserelin

label_protocol: Total RNA was converted into double-stranded cDNA with the Superscript Choice System (Invitrogen, Carlsbad, CA, USA) using an oligo-dT primer containing a T7 RNA polymerase promoter (Genset, Evry, France). The cDNA was used as a template for an in vitro transcription reaction to synthesize biotin-labeled antisense cRNA (BioArray High Yield RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY, USA).

extract_protocol: TriReagent followed by DNase treatment

value: Vastus lateralis

value: male

tag: treatment

value: Goserelin


title: Goserelin, Subject-Y


title: Genomic DNA from monocyte_2

description:
Sample 2
monocyte isolated from human blood


title: HUF86P4, vehicle + NOTCH1 shRNA

description: Gene expression data from HUF86P4 without EPC treatment, transfected with NOTCH1 shRNA plasmid


title: Goserelin, Subject-OE


title: Goserelin, Subject-C


title: Placebo, Subject-O

source_name: Vastus lateralis muscle 4 hours after last strength training session, placebo

value: Placebo


title: Placebo, Subject-R


title: Goserelin, Subject-T


title: 35S::VvMYBC2-L3_Hairy roots_Maccabeu_rep1

city: Verona

first: Erika

last: Cavallini

state: Verona

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

description: Hairy roots expressing 35S::VvMYBC2-L3 of Vitis vinifera cv Maccabeu, replicate 1

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Vitis vinifera

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: The in vitro plantlets and the transgenic and wild type hairy roots were grown under light and temperature controlled.

extract_protocol: the  hairy roots were sampled and then frozen in liquid nitrogen. All samples were stored at -80oC. Total RNA was extracted using the RNeasy Plant Mini kit (Qiagen) following the manufacturer’s protocol.

treatment_protocol: For overexpression of VvMYBC2-L3 in Vitis vinifera cv Maccabeu hairy roots, the cDNA sequence was transferred into the binary vector pH2GW7 by site-specific recombination. The construct was then inserted into Agrobacterium tumefaciens A4 by electroporation and used for the grapevine transformation.

tag: cultivar

value: Maccabeu

value: Hairy roots


title: Muscle_control_2

city: Sendai

first: Naoki

last: Suzuki

state: Miyagi

address: 1-1 Seiryo-machi, Aoba-ku

department: Department of Neurology

country: Japan

institute: Tohoku University School of Medicine

description: We followed manufacturer's protocol.

hyb_protocol: We followed manufacturer's protocol. http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

scan_protocol: We followed manufacturer's protocol, and used GenePix 4000B. http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

data_processing:
CodeLink Expression Analysis v5.0 software (Applied Microarrays, Inc.) was used for quantification.
MicroArray Data Analysis Tool (Filgen, Inc.) was used for Normalization.

source_name: tibialis anterior Muscle control

extract_protocol: Qiagen RNeasy mini kit was used.

value: control

value: mlc1f-Cre/ Rpt3-floxed

value: female

value: tibialis anterior


title: 35S::VvMYBC2-L3_Hairy roots_Maccabeu_rep3

description: Hairy roots expressing 35S::VvMYBC2-L3 of Vitis vinifera cv Maccabeu, replicate 3


title: Placebo, Subject-K


title: 35S::VvMYBC2-L3_Hairy roots_Maccabeu_rep2

description: Hairy roots expressing 35S::VvMYBC2-L3 of Vitis vinifera cv Maccabeu, replicate 2


title: WT_Hairy roots_Maccabeu_rep3

description: Wild type hairy roots of Vitis vinifera cv Maccabeu (control), replicate 3

value: wild type


title: WT_Hairy roots_Maccabeu_rep2

description: Wild type hairy roots of Vitis vinifera cv Maccabeu (control), replicate 2


title: Placebo, Subject-B


title: Muscle_control_3

description: We followed manufacturer's protocol.

label_protocol:
We followed manufacturer's protocol.
http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf


title: Muscle_Rpt3 null_2

description: We followed manufacturer's protocol.

source_name: tibialis anterior Muscle homo

value: Rpt3 null


title: Muscle_Rpt3 null_3

description: We followed manufacturer's protocol.


title: Muscle_Rpt3 null_1

description: We followed manufacturer's protocol.


title: WT_Hairy roots_Maccabeu_rep1

description: Wild type hairy roots of Vitis vinifera cv Maccabeu (control), replicate 1


title: Muscle_control_1

description: We followed manufacturer's protocol.


title: B25MOL cells at passage 40, biological rep 2

status: Public on Sep 29 2014

city: Berlin

first: Kerstin

last: Heinrich

address: Fabeckstraße 30

institute: Mologen AG

description: Gene expression data from RCC cell line B25MOL at passages 40.

hyb_protocol: Following fragmentation  cRNA was hybridized for 16 hr at 45°C on Human GeneChip 1.0 ST. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Data of scanned GeneChips were transformed into nummeric data using Affymetrix Scanner Gene Chip Operating Software (GCOS).

data_processing: The data were analysed with the Bioconductor using RMA for preprocessing (background correction, summarization, normalization).

source_name: RCC cell line B25MOL at passage 40

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cell were cultivated under standard cell culture conditions (37°C, 95% humidity, 5 % CO2), in L-15 Leibovitz medium comprising follwoing additives 10% FCS, Pen/Strep, Sodiumcarbonat, L-Glutamin, D-Glucose, MEM vitamines.

extract_protocol: For total RNA extraction RNAzol was used according to manufactor's instruction.

treatment_protocol: Cells were harvested using 1´ Trypsin/EDTA and washed two times with PBS before subjected to RNA extraction.

tag: passage of cell line


title: B25MOL cells at passage 28, biological rep 2

description: Gene expression data from RCC cell line B25MOL at passages 28.

source_name: RCC cell line B25MOL at passage 28


title: B25MOL cells at passage 36, biological rep 2

description: Gene expression data from RCC cell line B25MOL at passages 36.

source_name: RCC cell line B25MOL at passage 36


title: B25MOL cells at passage 29, biological rep 1

description: Gene expression data from RCC cell line B25MOL at passages 29.

source_name: RCC cell line B25MOL at passage 29


title: B25MOL cells at passage 36, biological rep 1


title: B25MOL cells at passage 40, biological rep 1


title: B25MOL cells at passage 28, biological rep 1


title: B25MOL cells at passage 29, biological rep 2


title: Islets-NODRagko-8wk_4

city: St. Louis

first: Javier

middle: A

last: Carrero

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

institute: Washington University School of Medicine

description: Sample name: NODRagko-8wk-4

hyb_protocol: GeneChip Fluidics Station 450

scan_protocol: GeneChip Scanner 3000 7G

data_processing:
Expression Console for Quality Control, Arraystar for robust multi-array analysis with quantile normalization for normalization of data, Combat for batch effect correction.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.na32.mm9.probeset.csv

source_name: Islets of Langerhans

label_protocol: Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay

growth_protocol: Specific pathogen-free barrier animal facility.

extract_protocol: Ambion RNAqueous.

treatment_protocol: None.

tag: background strain

value: NOD/ShiLt

tag: genotype

value: pancreatic islets of Langerhans


title: B25MOL cells at passage 20, biological rep 2

description: Gene expression data from RCC cell line B25MOL at passages 20.

source_name: RCC cell line B25MOL at passage 20

tag: cell line


title: Islets-NODRagko-8wk_5

description: Sample name: NODRagko-8wk-5


title: Islets-NODRagko-8wk_6

description: Sample name: NODRagko-8wk-6


title: Islets-NODRagko-8wk_3

description: Sample name: NODRagko-8wk-3


title: Islets-NODBatf3ko-8wk_4

description: Sample name: NODBatf3ko-8wk-4


title: Islets-NODBatf3ko-8wk_5

description: Sample name: NODBatf3ko-8wk-5


title: Islets-NOD-8wk_6

description: Sample name: NOD-8wk-6

value: NOD


title: Islets-NOD-8wk_3

description: Sample name: NOD-8wk-3


title: Islets-NOD-8wk_5

description: Sample name: NOD-8wk-5


title: B25MOL cells at passage 20, biological rep 1


title: Islets-NODBatf3ko-8wk_2

description: Sample name: NODBatf3ko-8wk-2


title: Islets-NODBatf3ko-8wk_3

description: Sample name: NODBatf3ko-8wk-3


title: Islets-NODRagko-8wk_2

description: Sample name: NODRagko-8wk-2


title: Islets-NOD-8wk_2

description: Sample name: NOD-8wk-2


title: Islets-NODBatf3ko-8wk_6

description: Sample name: NODBatf3ko-8wk-6


title: Islets-NODRagko-8wk_1

description: Sample name: NODRagko-8wk-1


title: Islets-NODRagko-6wk_3

description: Sample name: NODRagko-6wk-3


title: Islets-NOD-8wk_1

description: Sample name: NOD-8wk-1


title: OASF_2_pcDNA-tbx5

city: Schlieren

first: Emmanuel

last: Karouzakis

address: Wagistrasse 14/3.OG

department: Center of Experimental Rheumatology

country: Switzerland

institute: University Hospital Zurich

hyb_protocol: The hybridization, washing and staining was performed using the Affymetrix kit.

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000.

data_processing: Data have been processed using simpleaffy and xmacore packages of bioconductor and the exon.pmcdf1.0 chip definition from annmap.picr.man.ac.uk

label_protocol: The labeled cDNA was hybridized to the Human Genome U133 plus 2.0 gene expression array (Affymetrix) using the Fluidics Station 450.

growth_protocol: Synovial tissue specimens were obtained from OA patients undergoing joint replacement surgery . They were homogenized and digested in 150 mg/ml dispase II  at 37 °C for 60 min.

extract_protocol: After 48h, RNA was extracted using the RNeasy Miniprep kit (Qiagen).

treatment_protocol: OASF (n=2) cultures were transfected with 2µg of pcDNA3.1(+)_TBX5 or pcDNA3.1(+) empty vector as a negative control using the Basic Nucleofector kit for primary human fibroblasts (Amaxa/Lonza).

tag: cell type

value: Osteoarthritis synovial fibroblasts (OASF)

tag: passage

value: 4-5 (primary culture)

tag: transfected with

tag: genotype/variation

value: TBX5 overexpression


title: OASF_1_pcDNA-tbx5


title: Islets-NOD-8wk_4

description: Sample name: NOD-8wk-4


title: OASF_1_pcDNA

value: pcDNA3.1(+) empty vector

value: vector control


title: Islets-NODBatf3ko-8wk_1

description: Sample name: NODBatf3ko-8wk-1


title: Islets-NOD-6wk_1

description: Sample name: NOD-6wk-1


title: Islets-NODRagko-6wk_1

description: Sample name: NODRagko-6wk-1


title: Islets-NODRagko-6wk_2

description: Sample name: NODRagko-6wk-2


title: Islets-NODBatf3ko-6wk_2

description: Sample name: NODBatf3ko-6wk-2


title: Renal medulla of CPB pigs, biological rep 2

city: Bristol

first: Mohamed

middle: T.

last: Ghorbel

address: Level 7, BRI, Marlborough street

department: Bristol Heart Institute

country: United Kingdom

institute: University of Bristol

description: Gene expression data from pig renal medulla subjected to 2.5 of CPB under general anaesthesia

data_processing: RMA normalized using ArrayStar

organism: Sus scrofa

source_name: Renal medulla sample

label_protocol: One microgram of total RNA was processed to produce biotinylated cRNA targets using the Affymetrix protocol

extract_protocol: Ten to twenty milligrams of frozen renal medulla were homogenized and total RNA extracted using the Qiagen MiniElute protocol (Qiagen, UK).

treatment_protocol: Pigs were subjected to 2.5 hours of general anaesthesia or 2.5 hours of CPB under general anaesthesia. Renal medulla samples were collected 24 hours post intervention.

tag: breed

value: White-Landrace crossbred

value: Renal medulla sample

value: Pigs:subjected to 2.5 hours of CPB under general anaesthesia, renal medulla samples obtained 24hours post intervention


title: Islets-NOD-6wk_2

description: Sample name: NOD-6wk-2


title: Islets-NODBatf3ko-6wk_3

description: Sample name: NODBatf3ko-6wk-3


title: Islets-NODBatf3ko-6wk_1

description: Sample name: NODBatf3ko-6wk-1


title: Islets-NOD-6wk_3

description: Sample name: NOD-6wk-3


title: Control NCTC8626 biological rep 3

city: CARDIFF

last: Giles

address: Heath Park

institute: Cardiff University

description:
P. aueruginosa NCTC8626 C3
Gene expression data from untreated cells

hyb_protocol: As described by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 7G Autoloader

data_processing: The data were analyzed with Affymetrix Expression Console using the RMA algorithm

organism: Pseudomonas aeruginosa

source_name: P. aueruginosa grown for 4 hours in MHB

label_protocol: As described by Affymetrix

growth_protocol: Cells harvested after 4 hours growth in MHB at 37°C

extract_protocol: Extraction of RNA was done following manufacturers instructions using SV Total RNA extraction Sytem, Promega

treatment_protocol: Test cells were treated with 10% (w/v) manuka honey for the 4 hour incubation period

tag: agent

value: control


title: Honey treated NCTC8626 biological rep 1

description:
P. aueruginosa NCTC8626 H1
Gene expression data from honey treated cells

source_name: P. aueruginosa grown for 4 hours in MHB with 10% manuka honey

value: honey


title: Control NCTC8626 biological rep 2

description:
P. aueruginosa NCTC8626 C2
Gene expression data from untreated cells


title: Honey treated NCTC8626 biological rep 2

description:
P. aueruginosa NCTC8626 H2
Gene expression data from honey treated cells


title: Honey treated NCTC8626 biological rep 3

description:
P. aueruginosa NCTC8626 H3
Gene expression data from honey treated cells


title: Control NCTC8626 biological rep 1

description:
P. aueruginosa NCTC8626 C1
Gene expression data from untreated cells


title: Renal medulla of CPB pigs, biological rep 1


title: Renal medulla of CPB pigs, biological rep 3


title: heart_Acsl1flox_rep3

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

description: Biological replicate 3 of 3

hyb_protocol: Cy-5 labeled cRNA was co-hybridized to Agilent 014868 Whole Mouse Genome Microarrays with equimolar amounts of Cy-3 labeled WMRR-derived cRNA. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.  After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Axon Instruments GenePix 4000b scanner and processed using Agilent FeatureExtractor 9.5.3.1.

data_processing: Data files uploaded into Genespring 12.4. Probes were lowess normalized and combined at a gene-level. Genes that were not present in at least two of the biological replicates per genotype were filtered and removed.

source_name: Whole Mouse Reference RNA (WMRR)

label_protocol: 500 ng of WMRR or heart RNA labeled with Cy-3 or Cy-5, respectively (Perkin Elmer) and amplified using the Low Input RNA Amplification Kit (Agilent) as described by the manufacturer.

growth_protocol: At 6 to 8 wk of age, Acsl1H-/- and littermate Acsl1flox/flox control male mice were injected i.p. with tamoxifen (Sigma, St. Louis MO) (75 mg/kg BW), dissolved in corn oil (20 mg/ml) for 4 consecutive days (3 mg/40 g body weight).

extract_protocol: Total RNA was isolated from heart ventricles using RNeasy Fibrous Tissues Kit (Qiagen) following manufacturer's instructions

treatment_protocol: Ten weeks after tamoxifen induction, heart ventricles were removed and snap frozen in liquid nitrogen

tag: develolpmental stage

value: neonatal

tag: tissue type

value: whole animal

value: mixed 129Sv and C57BL/6

source_name: heart, 10 week post tamoxifen


title: Renal medulla of Sham pigs, biological rep 1

description: Gene expression data from pig renal medulla subjected to 2.5 of general anaesthesia

tag: tissue

value: Pigs:subjected to 2.5 hours of general anaesthesia, renal medulla samples obtained 24hours post intervention


title: heart_Acsl1H-/-_rep2

description: Biological replicate 2 of 4

tag: strain


title: heart_Acsl1H-/-_rep3

description: Biological replicate 3 of 4


title: Cj_summer_20120731-24:00_rep2

city: Hitachi

first: Mine

last: Nose

state: Ibaraki

address: 3809-1 Ishi, Juo

institute: Forest Tree Breeding Center

hyb_protocol: Hybridized at 42 °C during 17 h with three μg of Cy3 labeled ds-cDNA in the NimbleGen hybridization system.

scan_protocol: Slides were scanned at 2 μm/pixel resolution using an NimbleGen MS 200 scanner (NimbleGen).

data_processing: Scanned images (TIFF format) were imported into the NimbleScan software version 2.6 (NimbleGen) for grid alignment. The raw data (.pair file) was background correction as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).

organism: Cryptomeria japonica

label_protocol: Ten micrograms of total RNA were transcribed to double strand (ds) cDNA using a Superscript ds-cDNA synthesis kit (Invitrogen, Carlsbad, CA, USA) and  labeled by a NimbleGen One-Color Labeling Kit (NimbleGen, Madison, WI, USA)  in accordance with the NimbleGen gene expression analysis protocol.

growth_protocol: Japanese cedar was propagated from a single tree by cutting, and grown for three years.

extract_protocol: A mixture of 10 cm of lateral branch apexes collected from three different branches was referred to as the shoot samples. Total RNA was extracted from 500 mg of sample as described in Gehrig et al. (2000) using an RNeasy Midi Kit (Qiagen, Hilden, Germany).

treatment_protocol: Potted cuttings were placed in outdoor location at Hitachi, Ibaraki 319-1301, Japan.

value: wild type

value: lateral branch apexes

tag: date of sampling

tag: sampling time


title: heart_Acsl1flox_rep1

description: Biological replicate 1 of 3


title: heart_Acsl1H-/-_rep4

description: Biological replicate 4 of 4


title: heart_Acsl1flox_rep2

description: Biological replicate 2 of 3


title: heart_Acsl1H-/-_rep1

description: Biological replicate 1 of 4


title: Cj_summer_20120731-24:00_rep1


title: Renal medulla of Sham pigs, biological rep 2

tag: treatment


title: Cj_summer_20120731-24:00_rep3


title: Cj_summer_20120731-20:00_rep3


title: Renal medulla of Sham pigs, biological rep 3


title: Cj_summer_20120731-20:00_rep1


title: EC_TNF_JQ1_3

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: gene expression of 2 hour JQ1 pre-treated followed by 1 hour TNF alpha treatment endothelium

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console. A CDF containing the ERCC probes was provided by Affymetrix.

data_processing: A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf. The data were analyzed with Bioconductor using the MAS5 nomalization method. Then, these data were renormalized to the external spike-ins. See manuscript for additional details.

source_name: HUVEC

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2009, Affymetrix).

growth_protocol: M199 + 20% FBS + 0.1% heparin + 50 micrograms/mL endothelial cell growth factors (ECGF).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.

treatment_protocol: Cells were stimulated with human TNFalpha (25 ng/mL, hr) in the presence or absence of JQ1 (500 nM, 2 hour pretreatment)

value: primary endothelium


title: Cj_summer_20120731-12:00_rep3


title: EC_TNF_JQ1_2


title: EC_TNF_3

description: gene expression of 1 hour TNF alpha treated endothelium


title: Cj_summer_20120731-16:00_rep3


title: Cj_summer_20120731-16:00_rep1


title: Cj_summer_20120731-08:00_rep2


title: OASF_2_pcDNA

value: Osteoarthritis synovial fibroblasts (OASF)


title: EC_TNF_2


title: Cj_summer_20120731-12:00_rep2


title: EC_TNF_JQ1_1


title: Cj_summer_20120731-20:00_rep2


title: Cj_summer_20120731-08:00_rep3


title: Cj_summer_20120731-16:00_rep2


title: Cj_summer_20120731-12:00_rep1


title: EC_TNF_1


title: EC_JQ1_3

description: gene expression of JQ1 3 hour treated endothelium


title: Cj_summer_20120731-04:00_rep2


title: Cj_summer_20120731-04:00_rep3


title: EC_CONTROL_2

description: gene expression of control resting endothelium


title: EC_JQ1_1


title: EC_CONTROL_1


title: EC_CONTROL_3


title: Cj_summer_20120731-04:00_rep1


title: Cj_summer_20120730-24:00_rep1


title: dKO5DP

city: Memphis

first: Suzanne

middle: J

last: Baker

state: TN

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St Jude Children's Research Hospital

hyb_protocol: Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console Software v1.1

source_name: CBP/p300 null MEF 5, 3hr DP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: 10 cm dishes of each p4 wild type and CBP/p300 compound homozygous conditional MEF were plated at 1x10^6 cells/dish in 20ml DMEM+10%FBS containing Cre recombinase expressing adenovirus at an MOI of 100 and grown in a 3% O2 5%CO2 incubator.  Medium was changed 16hrs later for 10ml DMEM + 10%FBS and MEFs were grown for 48hrs in 3% O2 5%CO2 incubator.  MEFs were transferred to a normoxia 5% CO2 incubator and grown for 24hrs.

extract_protocol: RNA was isolated using the standard Trizol instructions.

treatment_protocol: 10ul of 100mM 2',2'-dipyridyl or ethanol vehicle was added to each plate and plates were returned to normoxia 5% CO2 incubator for 3hrs.  Medium was then removed from the plates and Trizol reagent was added directly to plate.

value: primary mouse embryonic fibroblast (e14.5)


title: Cj_summer_20120730-24:00_rep3


title: Cj_summer_20120731-08:00_rep1


title: Cj_summer_20120730-24:00_rep2


title: WT5DP

source_name: wild type MEF 5, 3h DP


title: Cj_summer_20120730-20:00_rep1


title: Cj_summer_20120730-20:00_rep3


title: EC_JQ1_2


title: L4-DRG, Sham, 23 days, (rep#1)

city: New York

first: Esperanza

last: Recio-Pinto

address: 180 Varick Street

department: Anesthesiology

institute: NYU

description: L: Lumbar; DRG: dorsal root ganglia; Sham

data_processing: For analysis only miRs that were detected in the 12 samples (12 arrays) were used.  MammU6-4395470, snoRNA135-4380912 and U87-4386735 were used as the reference miRs to obtain delta CT values for each of the miRs in each of the samples by using ExpressionSuite Software v1.0.3 (Applied Biosystems) and exported to an excel file.  In the text file, the “Fold_change_data.txt” values (the control sample) was used to obtain the “fold change” (2-delta deltaCT) of each miR in the experimental groups (Sural-SNI and Tibial-SNI).   This was done by subtracting the values between the corresponding DRGs (e.g. “L3-DRG-Sural-SNI#1 deltaCT” minus “ L3-DRG-Sham#1 deltaCT”, “L4-DRG-Sural-SNI#2 deltaCT” minus  “ L4-DRG-Sham#2 deltaCT” etc.). There was no outlier exclusion used.

source_name: Lumbar 4-Dorsal root ganglia

label_protocol: We used TaqMan Rodent Array Micro RNA Card-Av 2 (cat#4398967, Applied Biosystems, Life Technologies) in a 7900HT instrument from Applied Biosystems following the company  protocols (http://tools.lifetechnologies.com/content/sfs/manuals/4399721c.pdf)   and performed by the NYU Langone Genome Technology Center.

extract_protocol: The extraction of  totalRNA was done by using a phase separation with chloroform.

treatment_protocol: Under isoflurane anesthesia, the spared-nerve injury (SNI) was performed as previously described (Decosterd and Woolf, 2000). We used two different variations of the SNI: the Sural-SNI that consisted in the ligation and cutting of the common peroneal and the tibial nerve branches and the Tibial-SNI that consisted in the ligation and cutting of the common peroneal and the sural nerve branches. The ligated branches were transected distal to the ligature, and 2-3mm of each distal nerve branch stump was removed. In sham controls, the sciatic nerve and its branches were exposed but none of the branches were ligated or transected.

value: Sprague-Dawley

tag: gender

value: male

tag: weight

tag: developmental stage

value: adult


title: L3-DRG, Sham, 23 days, (rep#2)

source_name: Lumbar 3-Dorsal root ganglia


title: dKO1DP

source_name: CBP/p300 null MEF 1, 3hr DP


title: dKO5E

source_name: CBP/p300 null MEF 5, 3hr EtOH


title: L4-DRG, Tibial-SNI, 23 days, (rep#2)

description: L: Lumbar; DRG: dorsal root ganglia; Tibial-spared nerve injury


title: Cj_summer_20120730-16:00_rep3


title: WT3DP

source_name: wild type MEF 3, 3h DP


title: Cj_summer_20120730-20:00_rep2


title: Cj_summer_20120730-16:00_rep2


title: WT4DP

source_name: wild type MEF 4, 3h DP


title: WT4E

source_name: wild type MEF 4, 3h EtOH


title: dKO6E

source_name: CBP/p300 null MEF 6, 3hr EtOH


title: Cj_summer_20120730-12:00_rep3


title: Cj_summer_20120730-12:00_rep1


title: L4-DRG, Tibial-SNI, 23 days, (rep#1)


title: WT5E

source_name: wild type MEF 5, 3h EtOH


title: L3-DRG, Sham, 23 days, (rep#1)


title: Cj_summer_20120730-08:00_rep3


title: dKO1E

source_name: CBP/p300 null MEF 1, 3hr EtOH


title: L4-DRG, Sham, 23 days, (rep#2)


title: WT3E

source_name: wild type MEF 3, 3h EtOH


title: Cj_summer_20120730-12:00_rep2


title: Cj_summer_20120730-16:00_rep1


title: Cj_summer_20120730-08:00_rep2


title: L4-DRG, Sural-SNI, 23 days, (rep#2)

description: L: Lumbar; DRG: dorsal root ganglia; Sural-spared nerve injury


title: Cj_summer_20120730-04:00_rep3


title: L3-DRG, Tibial-SNI, 23 days, (rep#2)


title: fog-1 input rep3

city: Minneapolis

first: Caroline

last: Spike

state: MN

address: 420 Washington Avenue, SE

department: Genetics, Cell Biology, and Development

institute: University of Minnesota

description: RNAs present in the lysate

hyb_protocol: Hybridization and scanning were performed at the University of Minnesota Genomics Center using standard procedures and protocols described in the GeneChip Expression Analysis Technical Manual.

scan_protocol: Scanning was performed with a GeneChip Scanner 3000.

data_processing: The data were analyzed with Genespring GX12 using the default settings for MAS5.0

organism: Caenorhabditis elegans

source_name: Lysate RNA from sterile fog-1 adults

label_protocol: The MessageAmp III RNA Amplification kit (Ambion) was used to linearly amplify 500-600 nanograms input RNA or 3-5 microliters IP RNA and to fragment 20 micrograms aRNA.

growth_protocol: Embryos were hatched in the absence of food and raised on peptone-enriched plates seeded with NA22 at 25oC. Young adults were collected for lysate preparation approximately 48 hours after being placed on food.

extract_protocol: Lysates were clarified from sonicated animals. OMA-1-RNA complexes were isolated with antibody and eluted from the immunopurification matrix with AcTEV protease.  RNA was isolated from clarified lysates or OMA-1-RNA complexes using Trizol Reagent and purified with RNAqueous-Micro columns.

tag: genotype

tag: rip antibody


title: Cj_summer_20120730-08:00_rep1


title: fog-1 input rep2

description: RNAs present in the lysate


title: L3-DRG, Tibial-SNI, 23 days, (rep#1)


title: Cj_winter_20111223-24:00_rep1


title: Cj_winter_20111223-12:00_rep1


title: Cj_summer_20120730-04:00_rep2


title: Cj_summer_20120730-04:00_rep1


title: L3-DRG, Sural-SNI, 23 days, (rep#2)


title: L3-DRG, Sural-SNI, 23 days, (rep#1)


title: Cj_winter_20111222-24:00_rep1


title: Cj_winter_20111222-20:00_rep1


title: Cj_winter_20111222-16:00_rep1


title: spe-9 input rep1

description: RNAs present in the lysate

source_name: Lysate RNA from sterile spe-9 adults


title: fog-1 input rep1

description: RNAs present in the lysate


title: L4-DRG, Sural-SNI, 23 days, (rep#1)


title: Cj_winter_20111222-08:00_rep1


title: fog-1 OMA-1 IP rep3

description: RNAs that co-purify with OMA-1

source_name: OMA-1 IP RNA from sterile fog-1 adults

value: a-GFP (Novus Biologicals, NB600-308)


title: dKO6DP

source_name: CBP/p300 null MEF 6, 3hr DP

tag: cell type


title: spe-9 input rep3

description: RNAs present in the lysate


title: fog-1 OMA-1 IP rep1

description: RNAs that co-purify with OMA-1


title: spe-9 input rep2

description: RNAs present in the lysate


title: fog-1 OMA-1 IP rep2

description: RNAs that co-purify with OMA-1


title: spe-9 OMA-1 IP rep3

description: RNAs that co-purify with OMA-1

source_name: OMA-1 IP RNA from sterile spe-9 adults


title: spe-9 OMA-1 IP rep1

description: RNAs that co-purify with OMA-1


title: Cj_winter_20111222-04:00_rep1


title: Cj_winter_20111222-12:00_rep1


title: spe-9 OMA-1 IP rep2

description: RNAs that co-purify with OMA-1


title: AM WT adult biological rep2

status: Public on Sep 28 2014

city: Zurich

first: Christoph

last: Schneider

address: Otto-Stern-Weg 7

department: Department of Biology, Institute of Molecular Health Sciences

institute: ETH Zurich

description: mature AM

hyb_protocol: Samples were further hybridized for 20 hr at 48ºC on Affymetrix® Mouse Gene 1.1 ST Array Strip in the Affymetrix GeneAtlas Hybridization Station. Arrays were then washed and stained using Affymetrix GeneAtlas Fluidics Station.

scan_protocol: An Affymetrix GeneAtlas Imaging Station was used to measure the fluorescent intensity emitted by the labeled target.

data_processing: R (version 2.15.2)/Bioconductor (version 2.11) was used to perform RMA with package "affy".

source_name: AM from lungs of 2 adult PPARg fl/fl mice

label_protocol: Sense-stranded cDNA (5 µg) was fragmented and biotin-labeled according to the standard Affymetrix protocol (GeneChip® WT Terminal Labeling and Hybridization User Manual, 2011, Affymetrix)

extract_protocol: RNA was prepared from sorted populations using Trizol extraction and PureLink RNA Mini Kit (ambion, Life Technologies Co.) according to the manufacturer's instructions.

treatment_protocol: Organs were minced and digested with 2 mg/ml of type IV collagenase (Worthington) and 0.02 mg/ml DNaseI (Sigma) at 37°C for 45 minutes and subsequently passed through a 70 μm cell strainer. Cells were stained with eF780, anti-mouse CD45, CD11c, CD11b and Siglec-F. Mature AM were sorted as eF780-CD45+CD11chighautofluorescencehighSiglec-F+ and CD11blow or CD11bhigh from 11 days old or adult Ppargfl/fl and CD11c-Cre/Ppargfl/fl mice, respectively (BD FACSAria IIIu) and pre-AM (eF780-CD45+F4/80+CD11chigh and Siglec-FintCD11bint or Siglec-FlowCD11bhigh) were sorted from 2 days old mice.

tag: background strain


title: PDLSC_stretched_rep1

city: Miami

first: Herman

middle: S

last: Cheung

state: Florida

address: 1201 NW 16th Street

department: Geriatric Research, Education and Clinical Center

institute: Miami Veterans Affairs Medical Center

description: microRNA expression after 72 hours in 0.5μM nicotine-treated periodontal ligament-derived stem cells

hyb_protocol: The labeled samples were dried down by speed-vac for 2 hours and then resuspended by 18 ul DNase/RNase-free water. 4.5 ul 10x GE Blocking Agent and 22.5 ul 2x Hi-RPM Hybridization Buffer were added in each tube. The mixtures were incubated at 100oC for 5 minutes and then on ice water bath for 5 minetus. Finally, the samples were hybridized to Agilent SurePrint G3 Human miRNA Microarray Kit (Release 16.0) (G4870A) for 20 hours at 55°C in a rotating Agilent hybridization oven at 20 rpm.  After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned using the Agilent DNA Microarray Scanner (G2505C) and AgilentG3_miRNA profile was selected in Agilent Scan Control version A.8.4.1.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol:miRNA_107_Sep09 and Grid: 031181_D_F_20101116) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Periodontal ligament-derived stem cells, 0.5μM nicotine, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled samples were prepared from100 ng total RNAs using the miRNA Complete Labeling and Hybridization Kit according to the manufacturer's instructions.

growth_protocol: Human periodontal ligament-derived stem cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% heat-inactivated fetal bovine serum.

extract_protocol: Total RNA, including the microRNA fraction, was collected and extracted in TRIzol reagent according to the manufacturer's protocol (Invitrogen, Carlsbad, CA). The RNA concentration and quality were measured by Nanodrop 2000, whereas the RNA integrity was determined by the Agilent 2100 Bioanalyzer.

treatment_protocol: Human periodontal ligament-derived stem cells were cultured on collagen type 1-coated elastic silicone membranes and either subjected to a dynamic uniaxial mechanical strain protocol (2hr, 5% elongation, 0.5Hz) or left undisturbed. Mechanical strain was performed in a custom-built bioreactor designed in our laboratory. Cells were maintained in the same media used for growth protocol throughout the mechanical strain exposure.

tag: cell

value: Periodontal ligament-derived stem cells

value: 0.5μM nicotine


title: PDLSC_stretched_rep3

source_name: Periodontal ligament-derived stem cells, 0.5μM nicotine, replicate 3


title: AM KO adult biological rep2

description: arrested immature preAM

source_name: AM from lungs of 2 adult CD11cCre/PPARg fl/fl mice


title: AM WT adult biological rep1

description: mature AM


title: AM KO d11 biological rep1

description: arrested immature preAM

source_name: AM from lungs of 2 CD11cCre/PPARg fl/fl mice at d11 after birth


title: AM WT d11 biological rep2

description: mature AM

source_name: AM from lungs of 2 PPARg fl/fl mice at d11 after birth


title: AM KO d11 biological rep2

description: arrested immature preAM


title: PDLSC_stretched_rep2

source_name: Periodontal ligament-derived stem cells, 0.5μM nicotine, replicate 2


title: PDLSC_control_rep1

description: microRNA expression after 72 hours in 0μM nicotine-treated periodontal ligament-derived stem cells

source_name: Periodontal ligament-derived stem cells, 0μM nicotine, replicate 1

value: control


title: AM WT d11 biological rep1

description: mature AM


title: Hypertensive female_rep6

city: Penrith

first: Christine

middle: L

last: Chiu

state: New South Wales

address: Locked Bag 1797

department: School of Medicine

country: Australia

institute: Western Sydney University

description:
Gene expression data from female hypertensive kidneys
BPH2_Female_560

hyb_protocol: After fragmentation, ssDNA was hybridized for 17 hr at 45°C to GeneChip Mouse Gene 1.0 ST Arrays. Chips were washed and stained in the Affymetrix GeneChip® Fluidics Stations 450. For all of these steps, the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) was used according to the manufacturer’s recommendations (GeneChip® Whole Transcript (WT) Sense Target Labelling Assay Manual, version 4, Affymetrix)

scan_protocol: The chips were scanned using the GeneChip® Scanner 3000 7G 4C (Affymetrix) according to the manufacturer’s recommendations (GeneChip® Whole Transcript (WT) Sense Target Labelling Assay Manual, version 4, Affymetrix)

data_processing: Microarray results were normalized using robust multiarray analysis (RMA). Differentially expressed genes were identified for each sex using the comparative marker selection module in Genepattern which performs a two sided t-test

source_name: Mouse kidney female hypertensive

label_protocol: 100ng of total RNA was prepared for hybridization according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, version 4, Affymetrix)

growth_protocol: Mice were aged. At 12 weeks of age they were sacrificed by cervical dislocation

extract_protocol: Trizol extration of total RNA was performed according to manufacturer's instruction. Extracted RNA was purified using the Qiagen Rneasy Mini Kit (Qiagen, Germany) according to the manufacturer's instructions

treatment_protocol: Kidneys were extracted, rinsed in 1x PBS, snap frozen and stored at -80 degrees until processing.

value: Female

tag: disease state

value: hypertensive

value: kidney

tag: age

value: 12 weeks old


title: Hypertensive female_rep5

description:
Gene expression data from female hypertensive kidneys
BPH2_Female_559


title: PDLSC_control_rep2

source_name: Periodontal ligament-derived stem cells, 0μM nicotine, replicate 2


title: preAM KO d2 biological rep1

description: arrested preAM

source_name: AM from lungs of 2 CD11cCre/PPARg fl/fl mice at d2 after birth


title: AM KO adult biological rep1

description: arrested immature preAM


title: preAM WT d2 biological rep1

description: preAM

source_name: AM from lungs of 2 PPARg fl/fl mice at d2 after birth


title: Hypertensive female_rep4

description:
Gene expression data from female hypertensive kidneys
BPH2_Female_558


title: PDLSC_control_rep3

source_name: Periodontal ligament-derived stem cells, 0μM nicotine, replicate 3


title: Normotensive female_rep5

description:
Gene expression data from female normotensive kidneys
BPN3_Female_457

source_name: Mouse kidney female normotensive

value: normotensive


title: preAM KO d2 biological rep2

description: arrested preAM


title: Normotensive female_rep6

description:
Gene expression data from female normotensive kidneys
BPN3_Female_458


title: Hypertensive female_rep1

description:
Gene expression data from female hypertensive kidneys
BPH2_Female_542


title: Hypertensive female_rep2

description:
Gene expression data from female hypertensive kidneys
BPH2_Female_543


title: Normotensive female_rep4

description:
Gene expression data from female normotensive kidneys
BPN3_Female_455


title: Normotensive female_rep2

description:
Gene expression data from female normotensive kidneys
BPN3_Female_453


title: Normotensive female_rep3

description:
Gene expression data from female normotensive kidneys
BPN3_Female_454


title: preAM WT d2 biological rep2

description: preAM


title: Hypertensive female_rep3

description:
Gene expression data from female hypertensive kidneys
BPH2_Female_544


title: Normotensive female_rep1

description:
Gene expression data from female normotensive kidneys
BPN3_Female_452


title: Hypertensive male_rep6

description:
Gene expression data from male hypertensive kidneys
BPH2_Male_555

source_name: Mouse kidney male hypertensive

value: Male


title: Normotensive male_rep5

description:
Gene expression data from male normotensive kidneys
BPN3_Male_451

source_name: Mouse kidney male normotensive


title: Hypertensive male_rep2

description:
Gene expression data from male hypertensive kidneys
BPH2_Male_539


title: Normotensive male_rep6

description:
Gene expression data from male normotensive kidneys
BPN3_Male_456


title: Hypertensive male_rep5

description:
Gene expression data from male hypertensive kidneys
BPH2_Male_554


title: Normotensive male_rep4

description:
Gene expression data from male normotensive kidneys
BPN3_Male_450


title: Hypertensive male_rep1

description:
Gene expression data from male hypertensive kidneys
BPH2_Male_538


title: Normotensive male_rep3

description:
Gene expression data from male normotensive kidneys
BPN3_Male_449


title: Normotensive male_rep2

description:
Gene expression data from male normotensive kidneys
BPN3_Male_448


title: Hypertensive male_rep3

description:
Gene expression data from male hypertensive kidneys
BPH2_Male_540


title: Hypertensive male_rep4

description:
Gene expression data from male hypertensive kidneys
BPH2_Male_541


title: Normotensive male_rep1

description:
Gene expression data from male normotensive kidneys
BPN3_Male_447


title: 3544_day_0

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All datasets were normalized by using R (http://www.bioconductor.org). The raw data was log10 transformed before Z score transformation was performed [10]. The Z score was calculated for each sample by subtracting the overall mean gene intensity from the raw intensity signal for each gene. After that, this data was divided by the standard deviation of all of the measured intensities

source_name: Human whole blood

label_protocol: Biotinylated cRNA were pared with the Illumina TotalP RNA Amplification Kit for Illumina arrays

extract_protocol: Total RNA was extracted from whole blood drawn in pax-gene vacutainer tubes by PAX-gene RNA kit (Qiagen). Quality control was performed with NanoDrop 1000 instrument

tag: severity

value: Moderate

tag: virus type

value: Seasonal H1N1

tag: timepoint

value: Whole Blood


title: 3623_day_0

tag: tissue


title: 3631_day_28


title: 3628_day_0


title: 3544_day_28


title: 3624_day_0


title: 3631_day_0


title: 3543_day_0


title: 3542_day_28


title: 3542_day_0


title: 3543_day_28


title: 3628_day_28


title: 3626_day_28

value: Seasonal H3N2


title: 3251_day_0

value: Severe


title: 3623_day_28


title: 3535_day_0


title: 3541_day_28


title: 3541_day_0


title: 3535_day_28


title: 3239_day_28


title: 3624_day_28


title: 3078_day_0


title: 3626_day_0


title: 3077_day_0


title: 3078_day_28


title: 3076_day_28


title: 3251_day_28


title: 3239_day_0


title: 3077_day_28


title: 3076_day_0


title: 3064_day_0


title: 3070_day_0


title: 3062_day_0


title: 3074_day_0


title: 3058_day_28


title: 3070_day_28


title: 3074_day_28


title: 3062_day_28


title: 3058_day_0


title: 3046_day_28


title: 3067_day_28


title: 3046_day_0


title: 1424_day_28


title: 1423_day_0


title: 3064_day_28


title: 1424_day_0


title: 3067_day_0


title: 1422_day_0


title: 1423_day_28


title: 1422_day_28


title: 1420_day_28


title: 1421_day_28


title: 1417_day_28


title: 1419_day_28


title: 1418_day_28


title: 1418_day_0


title: 1420_day_0


title: 1416_day_28


title: 1417_day_0


title: 1414_day_28


title: 1415_day_0


title: 1023_day_0


title: 1408_day_0


title: 1421_day_0


title: 1414_day_0


title: 1022_day_0


title: 1410_day_28


title: 1021_day_28


title: 1410_day_0


title: 1019_day_0


title: 1019_day_28


title: 1017_day_0


title: 1017_day_28


title: 1018_day_28


title: 1020_day_28


title: 1408_day_28


title: 1016_day_28


title: 1014_day_28


title: 1416_day_0


title: 1014_day_0


title: 1013_day_0


title: 09K11743_DK3

value: OFI

value: Follow Up


title: 1011_day_0


title: 1012_day_28


title: 07K3605_DK3


title: 1023_day_28


title: 09K5037_DK3


title: 1011_day_28


title: 08K8478_DK3


title: 09K9518_DK3


title: 1021_day_0


title: 09K6390_DK3


title: 09K11331_DK3


title: 1012_day_0


title: 1020_day_0


title: 1419_day_0


title: 07K4393_DK3


title: 09K11728_DK3


title: 08K9922_DK3


title: 07K4363_DK3


title: 08K8482_DK3


title: 10K641_DK3


title: 10K20_DK3


title: 09K7938_DK3


title: 09K6386_DK3


title: 1016_day_0


title: 09K12016_DK3


title: 09K9877_DK3


title: 09K6744_DK3


title: 09K7942_DK3


title: 09K7933_DK3


title: 09K9880_DK3


title: 09K11250_DK3


title: 08K9937_DK3


title: 09K9884_DK3


title: 09K12020_DK3


title: 09K9882_DK3


title: 09K11751_DK3


title: 1010_day_0


title: 09K6749_DK3


title: 09K11235_DK3


title: 09K3353_DK3


title: 09K5978_DK3


title: 08K9923_DK3


title: 09K11332_DK3


title: 09K12011_DK3


title: 09K11742_DK3


title: 09K3262_DK3


title: 09K12024_DK3


title: 09K12032_DK3


title: 08K3137_DK3


title: 1018_day_0


title: 09K6380_DK3


title: 09K7952_DK3


title: 09K5979_DK3


title: 09K11730_DK3


title: 08K3130_DK3


title: 09K11343_DK3


title: 08K8507_DK3


title: 07K4366_DK3


title: 08K9927_DK3


title: 09K11739_DK3


title: 09K11344_DK3


title: 09K3237_DK3


title: 09K9889_DK3


title: 07K4378_DK3


title: 09K11336_DK3


title: 09K11733_DK3


title: 09K7519_DK3


title: 09K11735_DK3


title: 07K3658_DK3


title: 08K6578_DK3


title: 09K11754_DK3


title: 08K8484_DK3


title: 09K9891_DK3


title: 09K11274_DK3


title: 09K3245_DK3


title: 09K12009_DK3


title: 09K11326_DK3


title: 09K11736_DK3


title: 07K3607_DK3


title: 09K12012_DK3


title: 09K9513_DK3


title: 07K4372_DK3


title: 08K9921_DK3


title: 09K11240_DK3


title: 10K15_DK3


title: 08K8490_DK3


title: 09K11743_DK2

value: Acute


title: 09K11331_DK2


title: 08K8478_DK2


title: 09K5035_DK3


title: 09K9506_DK3


title: 08K8508_DK3


title: 07K4363_DK2


title: 07K4393_DK2


title: 08K9922_DK2


title: 09K5037_DK2


title: 09K12016_DK2


title: 09K9518_DK2


title: 10K641_DK2


title: 09K11728_DK2


title: 07K3605_DK2


title: 09K7938_DK2


title: 08K8504_DK3


title: 09K6744_DK2


title: 08K8482_DK2


title: 09K7942_DK2


title: 09K9884_DK2


title: 10K20_DK2


title: 09K6749_DK2


title: 09K6386_DK2


title: 09K7933_DK2


title: 09K9880_DK2


title: 08K9937_DK2


title: 09K11751_DK2


title: 08K8504_DK2


title: 09K11332_DK2


title: 09K9882_DK2


title: 09K9877_DK2


title: 09K11250_DK2


title: 09K11345_DK3


title: 09K3262_DK2


title: 08K9923_DK2


title: 09K12011_DK2


title: 09K3353_DK2


title: 09K12020_DK2


title: 09K5978_DK2


title: 09K11345_DK2


title: 09K12032_DK2


title: 09K6380_DK2


title: 09K11742_DK2


title: 09K12024_DK2


title: 07K4378_DK2


title: 09K3237_DK2


title: 08K3137_DK2


title: 08K8507_DK2


title: 09K11730_DK2


title: 09K11735_DK2


title: 09K11235_DK2


title: 09K11343_DK2


title: 09K11344_DK2


title: 09K5979_DK2


title: 08K3130_DK2


title: 08K6578_DK2


title: 08K9927_DK2


title: 07K3658_DK2


title: 09K3245_DK2


title: 09K11754_DK2


title: 09K12009_DK2


title: 09K11739_DK2


title: 07K4366_DK2


title: 09K9889_DK2


title: 09K3240_DK3


title: 09K7519_DK2


title: 09K7952_DK2


title: 09K11336_DK2


title: 09K11736_DK2


title: 07K3607_DK2


title: 09K9891_DK2


title: 09K11733_DK2


title: 09K11240_DK2


title: 07K3614_DK2


title: 09K5035_DK2


title: 08K8490_DK2


title: 09K11274_DK2


title: 07K4372_DK2


title: 09K9521_DK3

value: Mild


title: 08K9921_DK2


title: 08K8484_DK2


title: 09K3240_DK2


title: 08K8508_DK2


title: 09K7521_DK3


title: 10K15_DK2


title: 09K3350_DK3


title: 09K9513_DK2


title: 08K3127_DK3


title: 08K6584_DK3


title: 09K11326_DK2


title: 09K9506_DK2


title: 09K12012_DK2


title: 09K5968_DK3


title: 08K3121_DK3


title: 09K3348_DK3


title: 07K3655_DK3


title: 09K6746_DK3


title: 07K3654_DK3


title: 09K11752_DK3


title: 07K4371_DK3


title: 09K3261_DK3


title: 09K3351_DK3


title: 08K8471_DK3


title: 09K9503_DK3


title: 09K3356_DK3


title: 08K3113_DK3


title: 07K3656_DK3


title: 09K11342_DK3


title: 10K14_DK3


title: 07K3643_DK3


title: 09K11272_DK3


title: 08K9949_DK3


title: 08K3109_DK3


title: 09K11740_DK3


title: 09K7936_DK3


title: 09K10986_DK3


title: 08K8470_DK3


title: 08K9943_DK3


title: 09K11340_DK3


title: 08K8483_DK3


title: 09K6751_DK3


title: 09K12021_DK3


title: 09K7943_DK3


title: 10K13_DK3


title: 08K3105_DK3


title: 08K8475_DK3


title: 09K11338_DK3


title: 09K7517_DK3


title: 07K3657_DK3


title: 09K11449_DK3


title: 09K7940_DK3


title: 07K3636_DK3


title: 09K11244_DK3


title: 09K11243_DK3


title: 08K6585_DK3


title: 09K5972_DK3


title: 09K11253_DK3


title: 09K3253_DK3


title: 09K3249_DK3


title: 09K3254_DK3


title: 09K6756_DK3


title: 09K12027_DK3


title: 09K3255_DK3


title: 09K11444_DK3


title: 09K3242_DK3


title: 09K6745_DK3


title: 09K5976_DK3


title: 09K3250_DK3


title: 09K5967_DK3


title: 08K6596_DK3


title: 09K5970_DK3


title: 09K6757_DK3


title: 09K12008_DK3


title: 09K6739_DK3


title: 08K9947_DK3


title: 09K12015_DK3


title: 09K11342_DK2


title: 09K9521_DK2


title: 09K11752_DK2


title: 07K3655_DK2


title: 08K3113_DK2


title: 09K3350_DK2


title: 09K5968_DK2


title: 08K8471_DK2


title: 09K3261_DK2


title: 09K7521_DK2


title: 09K11740_DK2


title: 07K3654_DK2


title: 09K3348_DK2


title: 08K9949_DK2


title: 09K6746_DK2


title: 07K4371_DK2


title: 08K6584_DK2


title: 08K9943_DK2


title: 08K8483_DK2


title: 09K3351_DK2


title: 09K9881_DK3


title: 08K3121_DK2


title: 08K3127_DK2


title: 09K11272_DK2


title: 10K14_DK2


title: 08K9936_DK3


title: 09K11338_DK2


title: 07K3656_DK2


title: 08K3105_DK2


title: 09K6751_DK2


title: 07K3643_DK2


title: 09K3356_DK2


title: rGBM10

city: Taipei

first: Shih-Hwa

last: Chiou

address: No. 201, Sec. 2, Shih-Pai Road

country: Taiwan

institute: Vghtpe

hyb_protocol: Hybridization was performed with 10x GE Blocking Agent and 2x Hi-RPM Hybridization Buffer according to the Agilent microRNA protocol in a Agilent SureHyb chamber loaded into a hybridization oven at 55°C rotating at 20 rpm for 20 hours.

scan_protocol: Microarrays were scanned immediately to reduce the impact of environmental oxidants on signal intensities using a High-resolution Agilent microarray scanner (Scan sitting: Values for 8×15k Formats, Scan region: Scan Area (61×21.6mm), Sac resolution (μm): 5,5μm scanning mode: Single Press, eXtended dynamic range (XDR): Selected, Dye channel: Green, Green photo-multiplier tube (PMT): XDR High 100%, XDR Low 5%).

data_processing: Data was processed using R software available at the VGHTPE.

source_name: recurrent Glioblastoma

label_protocol: 2 μl (100ng) of diluted total RNA was added to a 1.5ml Eppendorf tube and kept on ice. 2 μl of Calf Intestinal Alkaline Phosphatase (CIP) master mix was to total RNA. The reaction mixture was incubated in a heat block at 37 oC for 30 minutes. After that 2.8μl of 100% DMSO was added to each sample and incubated at 100 oC for 7 minutes. Samples were then immediately transferred to an ice-water bath, and 4.5μl of ligation master mix was added according to the protocol.

extract_protocol: Total RNA was extracted using the mirVanaTM kit (Ambion, TX) according to manufacturer's protocol.

value: recurrent GBM tissue


title: rGBM11


title: 09K7943_DK2


title: 09K11340_DK2


title: 08K8475_DK2


title: 07K3657_DK2


title: 09K12021_DK2


title: 10K13_DK2


title: 08K3109_DK2


title: 09K5976_DK2


title: 09K12027_DK2


title: 09K5972_DK2


title: 09K11449_DK2


title: 08K8470_DK2


title: 09K9503_DK2


title: 09K7936_DK2


title: 08K6585_DK2


title: rGBM12


title: 09K6756_DK2


title: 09K6739_DK2


title: 09K7517_DK2


title: 08K9947_DK2


title: 09K3251_DK3


title: 09K7940_DK2


title: 09K10986_DK2


title: 09K7934_DK3


title: rGBM7


title: rGBM8


title: rGBM9


title: rGBM4


title: rGBM5


title: rGBM6


title: GBM12

source_name: Glioblastoma

value: primary GBM tissue


title: rGBM1


title: rGBM2


title: rGBM3


title: 09K5970_DK2


title: 09K3249_DK2


title: GBM10


title: GBM11


title: 09K11253_DK2


title: 09K11244_DK2


title: 09K3253_DK2


title: 09K3251_DK2


title: 09K3255_DK2


title: 09K11243_DK2


title: 09K7934_DK2


title: GBM9


title: GBM7


title: 09K6745_DK2


title: GBM8


title: 09K3254_DK2


title: 07K3636_DK2


title: 09K11444_DK2


title: GBM5


title: GBM4


title: GBM3


title: GBM6


title: 09K12008_DK2


title: 09K3250_DK2


title: GBM1


title: GBM2


title: 09K3242_DK2


title: 09K5967_DK2


title: 08K9936_DK2


title: 08K6596_DK2


title: 09K6757_DK2


title: 09K12015_DK2


title: 09K9881_DK2


title: TE13 0h

status: Public on Sep 27 2014

city: Beijing

first: Qingtao

last: Hu

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics,Chinese Academy of Sciences

description: mRNA expression data from sensitive to radiation TE13

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: Cubic Spline

source_name: human esophageal squamous tissue

label_protocol: Reverse Transcription to Synthesize First Strand cDNA, Second Strand cDNA Synthesis, cDNA Purification, InVitro Transcription to Synthesize biotin-labeled cRNA, cRNA Purification

growth_protocol: Cells were cultured in high glucose RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum (HyClone) and 50 unit/ml penicillin and 50 µg/ml streptomycin.Cellswere maintained in a humidified incubator with 5% CO2 at 37 oC and split every 3-4 days. Tumor

extract_protocol: The RNA was extracted from each cultured cell line using SV Total RNA Isolation Kit (Promega) according to the manufacturer’s protocol. The extracted RNA was then treated with RNase-Free DNase set (QIAGEN) to remove any contaminating genomic DNA according to the manufacture’s protocol.

treatment_protocol: cell irradiation was carried out with a 6MV-X-ray linear accelerator.

tag: radiation sensitive or not

value: sensitive to radiation

value: esophageal

tag: cell line

tag: radiation time point

value: 0h of radiation


title: TE13 24h

value: 24h of radiation


title: 2.5mM_36d_Shoot

city: Urrbrae

first: Darren

last: Plett

state: South Australia

address: Hartley Grove Road

department: ACPFG

institute: University of Adelaide

description: Double stranded DNA was amplified by an in-vitro transcription reaction and labeled with Cy3 fluorescent dye. cRNA was hybridized to a custom 4x44K Maize Oligo Microarray.

hyb_protocol: Overnight hybridizations were performed with equal amounts of labelled cRNA to a custom 4x44K Maize Oligo Microarray from Agilent Technologies (Palo Alto, CA) according to Agilent’s One-Color Microarray-Based Gene Expression Analysis protocol. After hybridization, the microarray slides were washed.

scan_protocol: The microarray slides were immediately scanned with Agilent’s G2505C DNA Microarray Scanner. The images were visually inspected for image artefacts and feature intensities were extracted, filtered, and normalized with Agilent’s Feature Extraction Software (v10.5.1.1). Further quality control and downstream analysis was performed using data analysis tools in GeneData Analyst (v2.2.2).

data_processing: Cy3 median signal intensities were imported into R for further processing, omitting 4825 probes with no and very low fluorescent signals. The intensity values were log2 transformed and quantile normalized. Differently expressed genes were identified by the moderated t-statistic implemented in the LIMMA package (Smyth 2004). P-values were adjusted employing the method by Benjamini & Hochberg (1995) to control the false discovery rate (FDR). Genes were considered differentially expressed between the two conditions when their adjusted p-values were less or equal to 0.01.

organism: Zea mays

source_name: Nitrate treatment

label_protocol: Total RNA was treated with DNase-I followed by polyA RNA isolation (Illustra mRNA Purification Kit, GE Biosciences) for all samples. The total RNA and polyA RNA samples were visualized and quantified on Agilent’s Bioanalyzer 2100 to check for degradation and to determine final concentration. Each mRNA sample was made into double stranded DNA, amplified by an in-vitro transcription reaction and labelled with Cy3 fluorescent dye using Agilent’s Low RNA Input Fluorescent Linear Amplification Kit. The cRNA product was purified with Agencourt’s RNAClean Kit that utilizes SPRI (Solid Phase Reversible Immobilization) paramagnetic bead-based technology.

extract_protocol: Dwarf maize (Zea mays L. var Gaspe Flint) were grown in hydroponic systems as described previously (Garnett et al., 2013). Plants were sampled between 5 and 7 h after the start of the light period (06:00). The whole root and the youngest fully emerged leaf blade were excised, snap frozen in liquid N and stored at -80°C. Total RNA was extracted  from frozen tissue (Chomczynski, 1993), and 10 µg aliquots were prepared for microarray analysis. RNA integrity was checked on a 1.2% (w/v) agarose gel. Three biological replicates were analysed in all experiments.

tag: cultivar

value: Gaspe Flint

tag: treatment

value: Nitrate

tag: mm no3-

value: Shoot

tag: harvest day

tag: replicate

value: consists of 3


title: kyse170 24h

description: mRNA expression data from sensitive to radiation kyse170


title: TE13R 8h

description: mRNA expression data from non-sensitive to radiation TE13 cell line at 8h of radiation

value: non-sensitive to radiation

value: 8h of radiation


title: TE13R 24h

description: mRNA expression data from non-sensitive to radiation TE13 cell line at 24h of radiation


title: 0.5mM_36d_Shoot


title: kyse170R 8h

description: mRNA expression data from non-sensitive to radiation kyse170 cell line at 8h of radiation


title: Seg-1 24h

description: mRNA expression data from sensitive to radiation Seg-1


title: 2.5mM_29d_Shoot


title: kyse170 0h


title: TE13R 0h

description: mRNA expression data from non-sensitive to radiation TE13 cell line at 0h of radiation


title: Seg-1R 24h

description: mRNA expression data from non-sensitive to radiation Seg-1 cell line at 24h of radiation


title: Seg-1 8h


title: kyse170 8h


title: Seg-1R 8h

description: mRNA expression data from non-sensitive to radiation Seg-1 cell line at 8h of radiation


title: 2.5mM_18d_Shoot


title: 0.5mM_32d_Shoot


title: Seg-1 0h


title: Seg-1R 0h

description: mRNA expression data from non-sensitive to radiation Seg-1 cell line at 0h of radiation


title: 0.5mM_22d_Shoot


title: 2.5mM_15d_Shoot


title: 2.5mM_32d_Shoot


title: 0.5mM_29d_Shoot


title: 0.5mM_18d_Shoot


title: TE13 8h


title: 0.5mM_15d_Shoot


title: 2.5mM_22d_Shoot


title: 0.5mM_11d_Shoot


title: kyse170R 0h

description: mRNA expression data from non-sensitive to radiation kyse170 cell line at 0h of radiation


title: kyse170R 24h

description: mRNA expression data from non-sensitive to radiation kyse170 cell line at 24h of radiation


title: 2.5mM_11d_Shoot


title: WT_repl3

city: Zürich

first: Claus

middle: M

last: Azzalin

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

institute: ETH Zürich

hyb_protocol: Samples were hybridized to GeneChip S. pombe Tiling 1.0FR Array containing in total 1,160,624 probes at an average resolution of 20 bp (Affymetrix) according to manufacturer’s instructions.

scan_protocol: The arrays were scanned using an Affymetrix Scanner 3000 7G according to manufacturer's instruction.

data_processing:
The probes were remapped to the S.pombe genome build from May 2011 (available from ftp://ftp.ebi.ac.uk/pub/databases/pombase/pombe/Archived_directories/GFF/). The impact of the probe-level GC content and overall nucleotide composition on the observed expression values was eliminated using the normalization approaches implemented in the rMAT R package ("PairBinned" method, robust option). After this normalization, the expression values are on a natural log scale.
The result files (.txt) contain the normalized expression values (on a natural log scale) for the individual probes in each of the samples.

label: DNA labeling reagent (Affymetrix)

organism: Schizosaccharomyces pombe

source_name: total RNA extracts of wildtype yeast

label_protocol: Labeled cDNA libraries were constructed according to the GeneChip Eukaryotic Double Strand Whole Transcript Protocol (Affymetrix). In short, total RNA from three biological replicates was reverse transcribed with random primers and SuperScript II (Invitrogen) before performing second strand cDNA synthesis with Klenow fragment (New England Biolabs). Reverse transcription and second strand synthesis were performed in presence of dUTP to allow subsequent fragmentation with Uracil-DNA glycosylase and human apurinic/apyrimidinic endonuclease 1 (Affymetrix). Fragmented double stranded cDNA was labeled with DNA labeling reagent and terminal deoxynucleotidyl transferase.

growth_protocol: Three biological replicates of wildtype and cay1D cells were cultured to exponential phase OD(595)=0.8 in standard yeast extract medium with supplements (YES) at 30°C

extract_protocol: Total RNA was extracted from yeasts grown to exponential phase using the hot phenol method (Schmitt et al, 1990, Nucleic Acid Research 18: 3091-2) and subjected to 2 DNaseI (QIAGEN) digestion steps. RNA quality was assayed using a 2100 Bioanalyzer (Agilent).

treatment_protocol: untreated

tag: strain


title: Cay1D_repl1

source_name: total RNA extracts of cay1D yeast

value: h- cay1D::kanMX6


title: Cay1D_repl2


title: 2.5mM_36d_Root

value: Root


title: WT_repl1


title: 2.5mM_32d_Root


title: Group1 - MNCs from PMF patients - Replicate 2

city: Rome

first: fiorella

last: ciaffoni

state: Italy

address: Viale Regina Elena 299

department: Cellular Biology and Neurosciences

institute: Istituto Superiore di Sanità

description: Test

data_processing:
Three different subjects were analyzed per experimenalt point (replicate 1, 2 and 3). Differences in gene expression among groups were identified using the RT 2 Profiler PCR Array Data Analyses Web portal (QIAGEN) and considered statistically significant with a p<0.05 by two-tailed, Student’s t-test.
For the normalization it was used the average of GAPDH as housekeeping gene.
Target gene signals (Ct value cut-off 35) normalized to housekeeping gene; 2^-(Ave deltaCt), where deltaCt = (Ct_Target − Ave(Ct_HKG).
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Biological consequences of gene expression alterations were predicted with the David Bioinformatic Database (David Bioinformatics Resources 6.7 NIAID/NIH)
Normalized data file reports normalized signal (against housekeeping genes) (2^(-Avg.(Delta(Ct)))
Fold Change file reports test/control (i.e., Group1/Control Group) ratios.

label: SYBR Green

source_name: bone marrow

label_protocol:
PCR assays were performed using the Human TGFβ/BMP Signaling Pathway PCR array (PAHS-035ZA - SABiosciences, Frederick, MD). Reverse transcription was performed from 500 ng total RNA using RT2 First Strand kit  (SABiosciences, Frederick, MD) following manufacturer's instructions.
RT-PCR was performed with RT2 SYBR ROX qPCR Mastermix (SABiosciences, Frederick,MD) following manufacturer's instructions
Absolute quantification was detected by 7300 Real-TimePCR System (Applied Biosystem).Termal cycling conditions were setted following manufacturer's instructions

extract_protocol: MNCs of patients with PMF were obtained by bone marrow aspirate followed by centrifugation on Ficoll Hypaque density gradient.

value: bone marrow

tag: cell type

value: mononuclear cells

tag: sample

tag: Sex

value: F

tag: diagnosis (who)

value: PMF

tag: genotype

value: JAK2V617F (hetero)

tag: dipss score at sampling

value: Int-1 risk

tag: date of sampling


title: 0.5mM_29d_Root

tag: tissue


title: WT_repl2


title: 2.5mM_11d_Root


title: 0.5mM_22d_Root


title: 2.5mM_18d_Root


title: 0.5mM_18d_Root


title: Group1 - MNCs from PMF patients - Replicate 3

description: Test

tag: age


title: Group1 - MNCs from PMF patients - Replicate 1

description: Test

value: High risk


title: Control Group - MNCs from healthy subject - Replicate 3

description: Control

value: BM3527 ALLCELLS, Emeryville, CA

value: healty subject

value: WT


title: 0.5mM_15d_Root

value: Gaspe Flint

value: Nitrate


title: 2.5mM_22d_Root

value: consists of 3


title: Control Group - MNCs from healthy subject - Replicate 2

description: Control

value: BM3600 ALLCELLS, Emeryville, CA


title: 557380A12 - NoDormancy_24h_Polysomal_BR3 vs Dormancy_24h_Polysomal_BR3

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Identification of transcripts that are differentially abundant (transcriptome) and transcripts that are addressed to translation (translatome) in imbibed Arabidopsis seeds in relation with dormancy. During imbibition of seeds (16h and 24h in darkness at 25°C, dormant and non-dormant seeds), transcriptome analysis is done on total RNA and translatome analysis on polysomal RNA.

hyb_protocol: Dormancy_24h_Polysomal_BR3 Cy5 / NoDormancy_24h_Polysomal_BR3 Cy3 : 30pmol.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seed - Media=soil Temperature=20°C/22°C Light=16h

treatment_protocol: Name:Dormancy+Imbibition_24h - time course study - temperature and imbibition,imbibition:time 24hour . At harvest dormant seeds are stored at -20°C. Total RNA and polysomal RNA (polysomal fractions purified on sucrose gradients) were extracted from imbibed seeds for 24h at 25°C in darkness.

tag: arabidopsis thaliana (columbia)  -  dev.stage (boyes et al. plant cell 2001)

treatment_protocol: Name:NoDormancy+Imbibition24h - time course study - temperature and imbibition,imbibition:time 24hour . Non-dormant seeds are obtained by after-ripening of dormant seeds: they are stored 3 weeks at 20°C at 56% relative humidity, and sored after at -20°C. Both type of seeds were imbibed 16h or 24h on water at 25°C.Total RNA and polysomal RNA (polysomal fractions purified on sucrose gradients) were extracted from imbibed seeds for 24h at 25°C in darkness.


title: 557380A11 - Dormancy_24h_Polysomal_BR3 vs NoDormancy_24h_Polysomal_BR3

hyb_protocol: NoDormancy_24h_Polysomal_BR3 Cy5 / Dormancy_24h_Polysomal_BR3 Cy3 : 30pmol.


title: 0.5mM_36d_Root