title: HaCaT_12Hr_ELF-EMF/8Hr_ELF-EMF

description:
Sample 3
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)


title: P9 - placebo day 14

status: Public on Mar 29 2014

type: RNA

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

country: USA

institute: Mount SinaiSchool of Medicine

description:
Group: placebo day 14
Type: Vivo

hyb_protocol: RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human skin biopsy

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion

tag: patient

value: healthy volunteer 9

tag: agent

value: placebo

tag: time

value: day 14

tag: tissue

value: skin biopsy


title: HaCaT_48Hr_ELF-EMF/Control2

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

description:
Sample 6
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)

hyb_protocol: Two-step hybridizations were performed. During the first hybridization, cDNA products was pipetted onto the array. Then, the array was incubated in the hybridization chamber in a water bath at 65℃ for 16 to 20 hours for the probe/target hybridization. At the second hybridization, the 3DNA dendrimer was pipetted onto the array and the array was submerged in a 65℃ water bath for only 2 to 3 hours for capture primer – 3DNA dendrimer hybridization. After hybridization, array was washed with SSC and SDS mixed buffer suggested by manufacturer's instruction of 3DNA array 50 kit.

scan_protocol: Microarrays were scanned by using GenePix 4100A (Axon, Foster City, CA) and images were taken at a resolution of 5μm. GenePix Pro 5.1 software was used to analyze image data.

data_processing: Spots were first selected by (1) excluding spots defined as flag or absent (2) keeping only channels with signal - background / SD of background greater than 1 (3) keeping spot diameter greater 75μm (4) eliminating spots with intensity CV greater than 100 in ether channel. The log ratio of the last spots were calculated and normalized by pin-wised LOWESS fit normalization.

source_name: Sample harvested at 48 h continuous ELF-EMF exposure

label_protocol: 3DNA Array 50 kit was used for fluorescence labeling on cDNA. Each total RNA (20μg) sample was reversely transcribed by Superscript II to single strand cDNA with the capture primer. cDNA was then purified by microcon YM-30 column.

growth_protocol: HaCaT cells were cultured in Dulbecco's Modified Eagle's Medium (Gibco BRL, Grand Island, NY) supplemented with 10% heat-inactivated fetal bovine serum (HyClone, Laboratories Inc., Logan, UT) and antibiotics (100 U/ml of penicillin, 100 μg/ml of streptomycin, 2mM L-glutamine; Gibco BRL, Grand Island, NY) at 37℃ in an incubator containing 5% CO2 humidified atmosphere.

extract_protocol: HaCaT cells were harvested with TRIzol reagent (Invitrogen) to extract total RNA according to the manufacture's protocols at scheduled time points. Total RNA were further purified by RNeasy (Quiagen). The quality of total RNA was assessed using the Agilent 2100 bioanalyzer with the RNA 6000 Nano LabChip kit (Agilent Technologies).

treatment_protocol: Cells were seeded in 10 cm cell culture dish and incubated for at least 12 hr before ELF-EMF exposure; following by continuous exposure at 1.5 mT, 60 Hz ELF-EMF for 4, 8, 12, 24, 48, 72 and 96 h without medium replacement.

tag: cell line

value: HaCaT

tag: gender

value: male

tag: age

value: 62 years

tag: cell type

value: in vitro spontaneously transformed keratinocytes

source_name: Control samples2


title: P9 - placebo day 3

description:
Group: placebo day 3
Type: Vivo

value: day 3


title: P9 - DPCP day 3

description:
Group: DPCP day 3
Type: Vivo

value: DPCP


title: HaCaT_24Hr_ELF-EMF/12Hr_ELF-EMF

description:
Sample 4
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)

source_name: Sample harvested at 24 h continuous ELF-EMF exposure

source_name: Sample harvested at 12 h continuous ELF-EMF exposure


title: P8 - placebo day 14

description:
Group: placebo day 14
Type: Vivo

value: healthy volunteer 8


title: P8 - DPCP late

description:
Group: DPCP late
Type: Vivo

value: late (between 4 and 8 month after the first visit)


title: HaCaT_8Hr_ELF-EMF/4Hr_ELF-EMF

description:
Sample 2
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)

source_name: Sample harvested at 8 h continuous ELF-EMF exposure

source_name: Sample harvested at 4h continuous ELF-EMF exposure


title: P8 - placebo day 3

description:
Group: placebo day 3
Type: Vivo


title: P8 - DPCP day 3

description:
Group: DPCP day 3
Type: Vivo


title: P8 - DPCP day 14

description:
Group: DPCP day 14
Type: Vivo


title: P6 - placebo day 3

description:
Group: placebo day 3
Type: Vivo

value: healthy volunteer 6


title: P6 - placebo day 14

description:
Group: placebo day 14
Type: Vivo


title: P6 - DPCP day 3

description:
Group: DPCP day 3
Type: Vivo


title: P21 - placebo day 3

description:
Group: placebo day 3
Type: Vivo

value: healthy volunteer 21


title: CGH: LD02-4485_v_Wm82

status: Public on Mar 30 2014

type: genomic

city: Saint Paul

first: Robert

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

hyb_protocol: Genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 9.1)

scan_protocol: Slides were scanned on the NimbleGen MS 200 Scanner (Roche/NimbleGen, Madison,WI) according to the array manufacturer instructions (NimbleGen CGH User Guild Ver 9.1)

data_processing: The segMNT algorithm in the NimbleScan software (verison 2.5) was used to extract the raw data and normalize into log2 ratio value according to the default settings.

molecule: genomic DNA

organism: Glycine max

source_name: DNA from soybean line LD02-4485

label_protocol: 500 ng of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 9.1.

growth_protocol: single plant leaf tissue

extract_protocol: Genomic DNA samples were isolated using the Qiagen Plant DNeasy protocol

tag: genotype

value: single plant leaf tissue

tag: strain

source_name: DNA from soybean line Wm82-ISU-01


title: P21 - placebo day 14

description:
Group: placebo day 14
Type: Vivo


title: P6 - DPCP late

description:
Group: DPCP late
Type: Vivo


title: P6 - DPCP day 14

description:
Group: DPCP day 14
Type: Vivo


title: P21 - DPCP day 3

description:
Group: DPCP day 3
Type: Vivo


title: CGH: Magellan_v_Wm82

source_name: DNA from soybean line Magellan

value: Magellan


title: CGH: Maverick_v_Wm82

source_name: DNA from soybean line Maverick

value: Maverick


title: CGH: S06-13640_v_Wm82

source_name: DNA from soybean line S06-13640


title: P16 - placebo day 3

description:
Group: placebo day 3
Type: Vivo

value: healthy volunteer 16


title: P20 - DPCP day 3

description:
Group: DPCP day 3
Type: Vivo

value: healthy volunteer 20


title: P9 - DPCP day 14

description:
Group: DPCP day 14
Type: Vivo

value: healthy volunteer 9

value: day 14


title: P20 - placebo day 14

description:
Group: placebo day 14
Type: Vivo

value: placebo

value: skin biopsy


title: P20 - DPCP day 14

description:
Group: DPCP day 14
Type: Vivo


title: P21 - DPCP day 14

description:
Group: DPCP day 14
Type: Vivo


title: P20 - placebo day 3

description:
Group: placebo day 3
Type: Vivo


title: P16 - placebo day 14

description:
Group: placebo day 14
Type: Vivo


title: CGH: LD00-3309_v_Wm82

source_name: DNA from soybean line LD00-3309


title: P16 - DPCP day 3

description:
Group: DPCP day 3
Type: Vivo


title: tPA-4

city: Sacramento

first: Glen

last: Jickling

state: CA

institute: University of California Davis

hyb_protocol: Each RNA sample was hybridized and scanned according to Nugen’s protocol onto Affymetrix Rat Genome 230 2.0 GeneChips (Affymetrix Santa Clara, CA)

scan_protocol: The arrays were washed and processed on a Fluidics Station 450 and scanned on a Genechip Scanner 3000.

data_processing: Raw expression values were imported into Partek software (Partek Inc., St. Louis, MO) and processed using GC-RMA normalization

label: Biotin

organism: Rattus norvegicus

label_protocol: Reverse transcription, amplification, and sample labeling were carried out using Nugen’s Ovation Whole Blood reagents (Nugen Teschnologies, San Carlos, CA).

extract_protocol: Blood was collected into PAXgene vacutainer tubes via cardiac puncture (PreAnalytiX, Germany). RNA was isolated using the PAXgene blood RNA kit (PreAnalytiX, Germany).

treatment_protocol: tPA 3.3mg/kg at 3hrs or control (no tPA).

tag: stress

value: control

value: tissue plasminogen activator (tPA)

value: blood

value: Sprague-Dawley

value: Male

tag: weight


title: CGH: LD01-5907_v_Wm82

source_name: DNA from soybean line LD01-5907


title: tPA-5


title: CGH: TN05-3027_v_Wm82

source_name: DNA from soybean line TN05-3027


title: P15 - placebo day 14

description:
Group: placebo day 14
Type: Vivo

value: healthy volunteer 15


title: P16 - DPCP late

description:
Group: DPCP late
Type: Vivo

value: DPCP

value: late (between 4 and 8 month after the first visit)


title: tPA-1


title: Normal-6

value: no tPA


title: tPA-2


title: CGH: CLOJ173-6-8_v_Wm82

source_name: DNA from soybean line CLOJ173-6-8

value: single plant leaf tissue


title: CGH: CLOJ095-4-6_v_Wm82

source_name: DNA from soybean line CLOJ095-4-6


title: tPA-3


title: P15 - placebo day 3

description:
Group: placebo day 3
Type: Vivo

source_name: human skin biopsy

value: day 3


title: Normal-5


title: P15 - DPCP day 14

description:
Group: DPCP day 14
Type: Vivo


title: Normal-3


title: tPA-6


title: Normal-4


title: P15 - DPCP day 3

description:
Group: DPCP day 3
Type: Vivo


title: CGH: LD02-9050_v_Wm82

source_name: DNA from soybean line LD02-9050


title: CGH: Prohio_v_Wm82

source_name: DNA from soybean line Prohio

value: Prohio


title: P14 - placebo day 14

description:
Group: placebo day 14
Type: Vivo

value: healthy volunteer 14


title: P14 - placebo day 3

description:
Group: placebo day 3
Type: Vivo


title: CGH: HS6-3976_v_Wm82

source_name: DNA from soybean line HS6-3976


title: P16 - DPCP day 14

description:
Group: DPCP day 14
Type: Vivo

value: healthy volunteer 16


title: CGH: 4J105-3-4_v_Wm82

source_name: DNA from soybean line 4J105-3-4


title: Normal-1


title: MCAO24T-4

value: permanent middle cerebral artery occlusion (MCAO)


title: P14 - DPCP late

description:
Group: DPCP late
Type: Vivo


title: Normal-2


title: MCAO24-6


title: MCAO24T-1


title: MCAO24T-5


title: MCAO24-4


title: P13 - DPCP day 14

description:
Group: DPCP day 14
Type: Vivo

value: healthy volunteer 13

value: day 14


title: MCAO24-3


title: MCAO24T-2


title: MCAO24T-6


title: MCAO24T-3


title: P14 - DPCP day 3

description:
Group: DPCP day 3
Type: Vivo

value: skin biopsy


title: MCAO24-1


title: P13 - placebo day 3

description:
Group: placebo day 3
Type: Vivo

value: placebo


title: P14 - DPCP day 14

description:
Group: DPCP day 14
Type: Vivo


title: MCAO24-2

value: blood


title: P13 - DPCP late

description:
Group: DPCP late
Type: Vivo


title: P13 - DPCP day 3

description:
Group: DPCP day 3
Type: Vivo


title: P13 - placebo day 14

description:
Group: placebo day 14
Type: Vivo


title: P12 - DPCP day 3

description:
Group: DPCP day 3
Type: Vivo

value: healthy volunteer 12


title: MCAO2T-6

value: 2 hours of middle cerebral artery occlusion (MCAO)

value: tissue plasminogen activator (tPA)

value: Sprague-Dawley

value: Male


title: P12 - DPCP day 14

description:
Group: DPCP day 14
Type: Vivo

value: DPCP


title: P12 - placebo day 3

description:
Group: placebo day 3
Type: Vivo


title: P12 - placebo day 14

description:
Group: placebo day 14
Type: Vivo


title: CGH: 5M20-2-5-2_v_Wm82

source_name: DNA from soybean line 5M20-2-5-2

value: single plant leaf tissue


title: MCAO24-5

value: no tPA


title: P1 - placebo day 3

description:
Group: placebo day 3
Type: Vivo

value: healthy volunteer 1

value: day 3


title: P1 - placebo day 14

description:
Group: placebo day 14
Type: Vivo


title: MCAO2T-4


title: MCAO2T-1


title: MCAO2-5


title: P1 - DPCP day 3

description:
Group: DPCP day 3
Type: Vivo


title: MCAO2T-3


title: MCF-10A cells, PDEF overexpression, biological rep1

city: Boston

first: Joan

middle: S.

last: Brugge

state: MA

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

hyb_protocol: Following fragmentation, 5 ug cRNA were hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array for 16 hrs.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneArray Chip Scanner, HP/Affymetrix Inc.

data_processing: Background correction and normalization of microarray data was performed using the Robust Multichip Average method implemented in the rma function of R/BioConductor. The differential expression was assessed using the empirical Bayes method implemented in BioConductor Limma package. The criteria for selecting differentially expressed genes was a false discovery rate (FDR)-corrected p-value of less than 0.05.

source_name: MCF-10A cells, PDEF overexpression

label_protocol: Biotinylated cRNAs were prepared according to the Affymetrix standard labeling protocol.

growth_protocol: Standard MCF10A growth conditions without EGF

extract_protocol: RNA-STAT 60 was used to prepare the RNA and Qiagen mini elute columns were used for purification

treatment_protocol: Retroviral infection for 26 hours

tag: treatment

value: PDEF overexpression


title: MCAO2-4


title: MCAO2T-2


title: MCAO2T-5


title: MCF-10A cells, PDEF overexpression, biological rep2


title: MCF-10A cells, vector control PDEF, biological rep3

source_name: MCF-10A cells, vector control

value: control


title: MCAO2-6


title: P1 - DPCP day 14

description:
Group: DPCP day 14
Type: Vivo


title: MCAO2-3


title: MCF-10A cells, vector control PDEF, biological rep1


title: MCAO2-1


title: MCF7, shRNA knockdown PDEF, biological rep2

hyb_protocol: 1.  The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed. 2.  The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.  3.  Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

source_name: MCF7 cells, shRNA targetting PDEF

label_protocol:
1.  RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.
 2.  The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.
 3.  The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range will not routinely be carried forward in the analysis. Should this occur, investigators would be notified and asked how they would like to proceed.
 4.  The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: Standard MCF7 growth conditions.

extract_protocol: Trizol reagent was used to prepare the RNA followed by additional purification using RNeasy from Qiagen.

treatment_protocol: Lentiviral infection and incubation in hormone depleted medium for 48 hours.

value: PDEF knockdown


title: MCF-10A cells, PDEF overexpression, biological rep3


title: MCF-10A cells, vector control PDEF, biological rep2


title: MCF7, shRNA knockdown PDEF, biological rep1


title: MCAO2-2


title: Anaes-3


title: MCF7, non specific control, biological rep1

source_name: MCF7 cells, non specific control


title: Anaes-2


title: Anaes-4


title: Anaes-6


title: P15 - DPCP late

description:
Group: DPCP late
Type: Vivo

value: healthy volunteer 15

value: late (between 4 and 8 month after the first visit)


title: MCF7, non specific control, biological rep2


title: Anaes-5


title: Anaes-1


title: Adipogenically differentiated cells day 15 replicate 3

city: Berlin

first: Mujib

last: Ullah

address: Charitéplatz 1 10117 Berlin, Virchoweg11

department: Berlin-Brandenburg Center for Regenerative Therapies, Dept. of Rheumatology

country: Germany

institute: Charité-University Medicine Berlin

description: Adipogenically differentiated cells were expanded in DMEM (4.5 g/l glucose) supplemented with 10% FBS, 20 mM HEPES buffer, 100 U/ml penicillin, 100 µg/ml streptomycin and 10 µg/ml insulin addationally containing, 1 µM dexamethasone, 0.2 mM indomethacin and 0.5 mM 3-isobutyl-1-methylxanthine.

hyb_protocol: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v5 protocol.

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

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de) and DAVID database (http://david.abcc.ncifcrf.gov/)

source_name: Cell culture: monolayer

label_protocol: 2 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix).

growth_protocol: Human mesenchymal stem cells (MSC) were obtained from 3 donors (normal donor) followed by adipogenic differentiation and then converted to dedifferentiation. MSC and dedifferentiated cells were expanded by cultivation in Dulbecco’s Modified Eagle Medium (DMEM), 10% selected fetal bovine serum (FBS), 20 mM HEPES buffer, 4 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin and 2 ng/ml basic fibroblast growth factor. While adipogenically differentiated cells were expanded in DMEM (4.5 g/l glucose) supplemented with 10% FBS, 20 mM HEPES buffer, 100 U/ml penicillin, 100 µg/ml streptomycin and 10 µg/ml insulin addationally containing, 1 µM dexamethasone, 0.2 mM indomethacin and 0.5 mM 3-isobutyl-1-methylxanthine.

extract_protocol: Total RNA from mesenchymal stem cells cultured in monolayer (passage 4), adipogenically differentiated cells and dedifferentiated cells was isolated applying protocols of the RNeasy Mini Kit (Qiagen, Hilden, Germany). For all sample culture, 1 ml TriReagent (Sigma-Aldrich) was added and stored at -80°C until further use. Frozen samples were transferred to room temperature for 15 min, and subsequently, 133 µl 1-Bromo-3-chloro-propane (Sigma-Aldrich) was admixed followed by centrifugation for 45 min at 13000xg. The aqueous phase was collected and nucleic acids were precipitated by addition of an equal volume ice-cold isopropanol. After 30 min incubation the precipitated nucleic acids were pelletized and resolved in 350 µl RLT buffer (Qiagen). Further purification was performed according to protocols for animal tissues of the RNeasy Mini Kit (Qiagen). RNA from each donor was separately handled; no pooling was done at any stage.

treatment_protocol: Human mesenchymal stem cells and dedifferentiiated cells were isolated from monolayer cell culture via  0.05 trypsin/1 mM EDTA in PBS for 5 min at 37°C, and adipogenically differentiated cells were isolated by 0.05 trypsin/1 mM EDTA for 0.05 trypsin/1 mM EDTA in PBS for 8 min at 37°C.

tag: donor/status

value: adipogenically differentiated cells

tag: cell culture

value: monolayer


title: Dedifferentiated cells day 7 replicate 2

description: Dedifferentiated were expanded by cultivation in Dulbecco’s Modified Eagle Medium (DMEM), 10% selected fetal bovine serum (FBS), 20 mM HEPES buffer, 4 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin and 2 ng/ml basic fibroblast growth factor.

value: dedifferentiated cells day 7


title: Dedifferentiated cells day 35 replicate 2

value: dedifferentiated cells day 35


title: Dedifferentiated cells day 7 replicate 1


title: Dedifferentiated cells day 35 replicate 3


title: Mouse embroynic stem cell line JM8

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from mouse embroynic stem cell line JM8

hyb_protocol: According to the Illumina expression protocol

data_processing: Normalized (quantile) data including background subtraction (GenomeStudioV2010.1 software, gene expression module version 1.6.0)

organism: Mus musculus

source_name: ESC

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion)

growth_protocol: Cell culture conditions as described in the paper; JM8 cells have been described in PMID:19525957; IDG3.2 have been described in PMID: 17586814

extract_protocol: RNeasy Mini Kit (Qiagen) including DNase treatment

treatment_protocol: No treatment

value: male


title: Dedifferentiated cells day 7 replicate 3


title: Dedifferentiated cells day 35 replicate 1


title: Adipogenically differentiated cells day 15 replicate 2


title: Mouse embroynic stem cell line IDG3.2

description: Gene expression data from mouse embroynic stem cell line IDG3.2

scan_protocol: According to the Illumina expression protocol

value: (129S6/svEvTac x C57BL/6J)


title: notochord_2 (miRNA)

city: Beijing, China

first: zhongjun

last: Liu

state: Beijing

address: 49 North Garden Rd, Haidian, 100191, Beijing, China.

department: Department of Orthopedics

country: China

institute: Peking University Third Hospital

description: miRNA expression data from notochord IVD of sample 2

hyb_protocol: Samples were prepared for hybridization using the GeneChip Hybridization Wash and Stain Kit (Affymetrix). Biotin-labeled RNA was mixed with Control Oligonucleotide B2, Eukaryotic Hybridization Controls and Hybridization Mix, and then was inject into miRNA 2.0 Arrays (Affymetrix). Hybridization was done in a GeneChip Hybridization Oven 645 (Affymetrix) for 16 to 18 hours, at 48°C, 60 rpm. Arrays were washed and stain with GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G with autoloader (Affymetrix). Raw data were generated with Affymetrix GeneChip Command Console

data_processing: Raw data from the generated .CEL files were imported into Affymetrix Expression Console using the RMA method

source_name: notochord,sample 2

label_protocol: RNA was tailed and labeled using the FlashTag™ Biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: All thesamples were stored at -80℃ until they were processed for RNA extraction in 1 batch

extract_protocol: Total RNA was isolated from PFPE samples by usingRecoverAllTM Total Nucleic Acid Isolation Kit (Life Technologies, Carlsbad, CA, USA) for mRNA and miRNA microarrayanalysis, according to the manufacturer’s instructions.Sample purity and integrity was confirmed by A260/A280 spectrophotometry and capillary gel electrophoresis on a Bioanalyzer 2100  (Agilent)

treatment_protocol: Paraffinsections from the fixed chordoma tissues were cut at 5 mm andstained with hematoxylin and eosin (H&E). All tissues were separated using laser capture microdissection(LCM)

value: Male

value: 25 weeks

value: embryo intervertebral disc


title: Mouse embryonic fibroblast

description: Gene expression data from mouse embryonic fibroblast

source_name: MEF

value: unknown


title: notochord_1 (miRNA)

description: miRNA expression data from notochord IVD of sample 1

source_name: notochord,sample 1

value: 27 weeks


title: iPSC, clone 78, biological replicate 1

description: Gene expression data from iPSC, biological replicate 9

source_name: iPSC


title: Adipogenically differentiated cells day 15 replicate 1


title: Undifferentiated mesenchymal stem cells replicate 3

description: MSC were expanded by cultivation in Dulbecco’s Modified Eagle Medium (DMEM), 10% selected fetal bovine serum (FBS), 20 mM HEPES buffer, 4 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin and 2 ng/ml basic fibroblast growth factor.

value: undifferentiated MSC


title: chordoam_2 (miRNA)

description: miRNA expression data from primary classic chordoma tissue of patient 2

source_name: chordoma,patient 2

value: 41 years

value: primary classic chordoma tissues


title: iPSC, clone 70, biological replicate 3

description: Gene expression data from iPSC, biological replicate 6

value: female


title: Undifferentiated mesenchymal stem cells replicate 2


title: iPSC, clone 78, biological replicate 2

description: Gene expression data from iPSC, biological replicate 10


title: Undifferentiated mesenchymal stem cells replicate 1


title: notochord_3 (miRNA)

description: miRNA expression data from notochord IVD of sample 3

source_name: notochord,sample 3

value: 24 weeks


title: chordoma_1 (miRNA)

description: miRNA expression data from primary classic chordoma tissue of patient 1

source_name: chordoma,patient 1

value: 50 years


title: iPSC, clone 78, biological replicate 3

description: Gene expression data from iPSC, biological replicate 8


title: wt_mouse_proBcells_cultured_2

city: Toronto

first: Paul

last: Kowalski

state: Ontario

address: PGCRL - 686 Bay St

department: Developmental and Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

description: Pro-B cells from wild type mice.

hyb_protocol: Hyb/wash was EukGE-WS2V4 protocol, using Affymetrix automated fluidics station, TCAG, Sick Kids.

scan_protocol: Arrays scanned on Affymetrix GeneChip Scanner 3000 by TCAG, Sick Kids.

data_processing: Scaling target signal was 150, used GCOS and MAS5.0 scaling for normalization.

source_name: wild type pro-B cells

label_protocol: cRNA was generated and labelled with biotin using the standard Affymetrix protocols, and hybridized to the Affymetrix Mouse Genome 430 2.0 array.

growth_protocol: Cells were isolated ex vivo from murine lymph nodes or cultured in vitro.

extract_protocol: Cells were isolated from murine lymph nodes with mechanical and protease disruption to generate a single cell suspension for flow sorting. After sorting, cells were lysed in TRIzol and RNA was extracted. Leukemic cell samples were a minimum of 85% CD19 positive by flow cytometry.

tag: strain/background

tag: genotype/variation

value: wild type

value: pro-B cells


title: wt_mouse_proBcells_cultured_3

description: Pro-B cells from wild type mice.


title: chordoma_3 (miRNA)

description: miRNA expression data from primary classic chordoma tissue of patient 3

source_name: chordoma,patient 3

value: 38 years


title: iPSC, clone 70, biological replicate 1

description: Gene expression data from iPSC, biological replicate 5


title: HaCaT_UVB/Control2

description:
Sample 19
human keratinocytes HaCaT were kindly provided from Dr. N.E. Fusening (German Cancer Research Center, Heidelberg, Germany)

source_name: Sample harvested at 8 h after 233 J/m2 UVB irradiation

value: HaCaT

value: 62 years

value: in vitro spontaneously transformed keratinocytes

source_name: Control samples2


title: A. lyrata 454

status: Public on Mar 28 2014

type: SRA

city: Gent

first: Marnik

last: Vuylsteke

address: Technologypark 927

department: Plant Systems Biology

country: Belgium

institute: VIB

library_source: transcriptomic

data_processing: trimmed reads and tag removed

organism: Arabidopsis lyrata

source_name: leaf

extract_protocol: Total RNA was isolated using Trizol Reagent (Life Technologies, Gaithersburg, MD)

value: leaf


title: double_mutant_leukemia_lymph_node_2

description: Leukemic blasts from double-knockout p53/PRKDC mice.

source_name: p53 -/-; Prkdc scid/scid double-mutant pre-B lymph node cells

value: mixed 129/Sv and BALB/C

value: p53 -/-; Prkdc scid/scid double-mutant

value: B-cell leukemia cells, arrested in pre-B-like stage


title: iPSC, clone 64, biological replicate 3

description: Gene expression data from iPSC, biological replicate 4

value: male


title: wt_mouse_proBcells_cultured_1

description: Pro-B cells from wild type mice.


title: iPSC, clone 48, biological replicate 2

description: Gene expression data from iPSC, biological replicate 2


title: iPSC, clone 64, biological replicate 1

description: Gene expression data from iPSC, biological replicate 11


title: double_mutant_leukemia_lymph_node_3


title: iPSC, clone 64, biological replicate 2

description: Gene expression data from iPSC, biological replicate 12


title: wt_mouse_preBcells_sorted_3

description: Pre-B cells from wild type mice.

source_name: wild type pre-B cells

value: pre-B cells


title: double_mutant_leukemia_lymph_node_1


title: chordoam_2 (mRNA)

description: gene expression data from primary classic chordoma tissue of patient 2

hyb_protocol: Samples were prepared for hybridization using the GeneChip Hyb Wash and Stain Kit (Affymetrix); mixed with Control Oligonucleotide B2, Eukaryotic Hybridization Controls and Hybridization Mix from and loaded to Human Gene ST 1.0 Arrays (Affymetrix). Hybridization was done in a GeneChip Hybridization Oven 640 (Affymetrix) for 17 hours, at +45°C, 60 rpm. Arrays were washed and PE-labeled on a GeneChip Fluidics Station 450 (Affymetrix)

label_protocol: Total RNA per sample was amplified using a SensationPlus™ FFPE Amplification and WT Labeling Kit (Affymetrix). Samples were subjected to the first strand cDNA synthesis, promoter synthesis, subsequent in vitro transcription of senseRNA, double-stranded cDNA synthesis, and labeling of cDNA. Total RNA was reverse transcribed to form the cDNA, purified with Purification Beads subsequently. Total cDNA was poly (dA) tailed on the 3´ end. A T7 dT oligo with a 3´ blocking group is hybridized to the 3´ (dA) tail. klenow and dNTP mix generate a double stranded T7 promoter region on the single stranded cDNA. The promoter-modified cDNA was in vitro transcribed to form RNA. The senseRNA was purified with purification beads and reverse transcribed using random primer mix. second strand cDNA was made with klenow and RNase H. Finally, the double-stranded cDNA was purified, fragmented and end-labeled

value: Male

value: 41 years


title: wt_mouse_preBcells_sorted_2

description: Pre-B cells from wild type mice.


title: chordoma_1 (mRNA)

description: gene expression data from primary classic chordoma tissue of patient 1

value: primary classic chordoma tissues


title: wt_mouse_preBcells_sorted_1

description: Pre-B cells from wild type mice.


title: iPSC, clone 48, biological replicate 3

description: Gene expression data from iPSC, biological replicate 3


title: chordoma_3 (mRNA)

description: gene expression data from primary classic chordoma tissue of patient 3


title: notochord_2 (mRNA)

description: gene expression data from notochord IVD of sample 2

value: 25 weeks

value: embryo intervertebral disc


title: notochord_3 (mRNA)

description: gene expression data from notochord IVD of sample 3

value: 24 weeks


title: notochord_1 (mRNA)

description: gene expression data from notochord IVD of sample 1

value: 27 weeks


title: iPSC, clone 48, biological replicate 1

description: Gene expression data from iPSC, biological replicate 1


title: iPSC, clone 70, biological replicate 2

description: Gene expression data from iPSC, biological replicate 7

value: female


title: control 1

city: jena

first: kolsoum

last: Inanloo Rahatloo

address: Beutenberg street 11

institute: Fritz Lipman Institute

description: Genomic DNA extracted from blood was genotyped using Infinium HumanCytoSNP-12  BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Illumina provide us .dat files and we analyzed them with GenomeStudio software. We excluded all zero SNPs. normalization and other processes  performed with GenomeStudio. We used Merlin Softwarewere for linkage analysis.

label: C-Bio and A-DNP

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from Blood was performed using proteinase K and repeated phenol-chloroform extraction.

value: Blood

tag: disease state

value: Healthy


title: CAD patient1

value: Female

value: Coronary Artery Disease


title: WG0087816-DNAH05_Weimaraner

city: Uppsala

first: Anna-Maja

last: Molin

address: Gerda Nilssons väg 2

department: Department of Animal Breeding and Genetics

country: Sweden

institute: Swedish University of Agricultural Sciences

hyb_protocol: standard Illumina protocols were used and hybridization was performed by Illumina Inc. USA

scan_protocol: standard Illumina protocols were used and scanning was performed by Illumina Inc. USA

data_processing:
Illumina Inc. USA performed the intial data processing (http://res.illumina.com/documents/products/datasheets/datasheet_caninehd.pdf). The standard cluster file that was used as reference when Log R ratios and B allele frequencies were calculated was created with the samples herein by Illumina Inc. USA. Further processing was perfromed by the authors using GenomeStudio V2010.3, Genotyping Module 1.8.4 where the Log R Ratio was corrected for GC content and low quality SNPs and intensity-only SNPs were removed. Remaining number of SNPs used in the CNV calling were 172115.
ID REF, LRR_GCC are Log R ratio values after GC-correction and this was used in the subsequent CNV discovery, Score, Theta, R, Gtype, B Allele Freq, Log R Ratio

organism: Canis lupus familiaris

source_name: blood

label_protocol: standard Illumina protocols were used and labelling was performed by Illumina Inc. USA

extract_protocol: genomic DNA was extracted from blood using standard procedures

tag: breed

value: Weimaraner

value: blood


title: control 2


title: CAD patient3


title: CAD patient5


title: WG0087816-DNAG11_Weimaraner


title: WG0087816-DNAH11_Weimaraner


title: CAD patient4


title: CAD patient6


title: CAD patient2


title: WG0087816-DNAF10_Weimaraner


title: WG0087816-DNAH12_Weimaraner


title: WG0087816-DNAH09_Weimaraner


title: WG0087816-DNAG12_Weimaraner


title: WG0087816-DNAH10_Weimaraner


title: WG0087816-DNAF12_Weimaraner


title: WG0087816-DNAG09_Weimaraner


title: WG0087816-DNAF11_Weimaraner


title: WG0087816-DNAG05_Weimaraner


title: BJ-EP4  [CNV]

city: Rochester

first: Hu

last: Li

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

description: Episomal protein induced iPS cells derived from Normal Human BJ fibroblast

hyb_protocol: Affymetrix Hybridization Oven 640 for 16 hrs at 50 deg C with rotation at 60 rpm. Washing and staining was done on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.

data_processing: For detecting CNV calls, the Affymetrix Genotyping Console 4.1.1 algorithm was used. CNV locations are based on the human genome assembly of March 2006 (hg18). Samples were normalized to Affymetrix HapMap reference dataset hybridized on the same platform. For CNV calls, regional GC correction, 10-kilobase (KB) cut-off value, and a minimum of ten markers were used as analysis configurations. All samples passed quality control requirements.  See supplementary file linked to Series record.

label_protocol: The DNA was prepared for hybridization to Affymetrix SNP 6.0 arrays according to the manufacturer's recommendations.

extract_protocol: Genomic DNA was purified with Qiagen Blood and Tissue DNA kit.

treatment_protocol: Not applicable

value: normal

tag: individual

value: control

value: Episomal protein induced iPS cells (BJ fibroblast-derived)

tag: passage


title: BJ-EP1  [CNV]

source_name: Episomal protein induced iPS cells derived from Normal Human BJ fibroblast


title: BJ-EP3  [CNV]


title: BJ  [CNV]

description: Normal Human BJ fibroblast

source_name: Normal Human BJ fibroblast

value: BJ fibroblast


title: hFib2 [CNV]

description: Human Normal Fibroblast

source_name: Human Normal Fibroblast

value: fibroblast


title: WG0087816-DNAE12_Weimaraner

tag: tissue


title: WG0087816-DNAE10_Weimaraner

tag: gender

value: Male


title: WG0087816-DNAG10_Weimaraner


title: WG0087816-DNAC10_Weimaraner


title: WG0087816-DNAD11_Weimaraner


title: H2-1 p6 [CNV]

description: Virus induced iPS cells passage6 derived from Normal Human fibroblast

value: Virus induced iPS cells (fibroblast-derived)


title: WG0093351-DNAG07_Terrier Yorkshire

value: Terrier Yorkshire


title: WG0087816-DNAC11_Weimaraner


title: H2-2 p6 [CNV]

source_name: Virus induced iPS cells passage6 derived from Normal Human fibroblast


title: WG0087816-DNAA11_Weimaraner


title: WG0087816-DNAE11_Weimaraner


title: WG0087816-DNAB12_Weimaraner


title: WG0087816-DNAA12_Weimaraner


title: BJ-EP2  [CNV]


title: WG0087816-DNAB10_Weimaraner


title: WG0093351-DNAH08_Terrier Yorkshire


title: WG0093351-DNAF07_Terrier Yorkshire


title: WG0093351-DNAF08_Terrier Yorkshire


title: WG0093351-DNAD08_Terrier Yorkshire


title: WG0093351-DNAH07_Terrier Yorkshire


title: WG0093351-DNAG08_Terrier Yorkshire


title: WG0093351-DNAB08_Terrier Yorkshire


title: WG0093351-DNAC08_Terrier Yorkshire


title: WG0087816-DNAC12_Weimaraner


title: STP032_Standard Poodle

value: Standard Poodle


title: WG0087816-DNAD12_Weimaraner


title: WG0093351-DNAA09_Terrier Yorkshire


title: STP017_Standard Poodle


title: STP002_Standard Poodle


title: STP016_Standard Poodle


title: STP012_Standard Poodle


title: STP021_Standard Poodle


title: STP009_Standard Poodle


title: WG0087816-DNAB11_Weimaraner


title: STP008_Standard Poodle


title: SHP031_Shar Pei

value: Shar Pei


title: STP007_Standard Poodle


title: SHP032_Shar Pei


title: STP018_Standard Poodle


title: SHP028_Shar Pei


title: WG0093351-DNAE08_Terrier Yorkshire


title: WG0093351-DNAA08_Terrier Yorkshire


title: SHP026_Shar Pei


title: SHP022_Shar Pei


title: SHP023_Shar Pei


title: STP001_Standard Poodle


title: SHP019_Shar Pei


title: SHP004_Shar Pei


title: SHP005_Shar Pei


title: SHP011_Shar Pei


title: STP024_Standard Poodle


title: WG0093351-DNAC07_Rottweiler

value: Rottweiler


title: SHP025_Shar Pei


title: WG0093351-DNAG06_Rottweiler


title: WG0093351-DNAF06_Rottweiler


title: WG0093351-DNAB07_Rottweiler


title: WG0093351-DNAH06_Rottweiler


title: WG0093351-DNAE07_Rottweiler


title: WG0093351-DNAA07_Rottweiler


title: WG0093351-DNAC06_Rottweiler


title: WG0093352-DNAH01_Poodles

value: Poodles


title: WG0093351-DNAD06_Rottweiler


title: WG0093352-DNAF01_Poodles


title: WG0093352-DNAA02_Poodles


title: WG0093351-DNAB06_Rottweiler


title: WG0093351-DNAE06_Rottweiler


title: WG0093352-DNAB01_Poodles


title: WG0093352-DNAE01_Poodles


title: WG0093351-DNAG12_Poodles


title: WG0093352-DNAD01_Poodles


title: WG0087816-DNAH02_Nova Scotia Duck Tolling Retriever

value: Nova Scotia Duck Tolling Retriever


title: WG0093352-DNAB02_Poodles


title: WG0087816-DNAG03_Nova Scotia Duck Tolling Retriever

value: Female


title: WG0087816-DNAH03_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAG04_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAH04_Nova Scotia Duck Tolling Retriever


title: WG0093351-DNAF12_Poodles


title: WG0093352-DNAC01_Poodles


title: WG0087816-DNAG02_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAH01_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAF05_Nova Scotia Duck Tolling Retriever


title: WG0093351-DNAH12_Poodles


title: WG0087816-DNAF04_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAF01_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAF02_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAE04_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAD04_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAE01_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAD05_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAF03_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAD03_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAE02_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAC05_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAE03_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAC04_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAC03_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAC01_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAC02_Nova Scotia Duck Tolling Retriever


title: WG0093351-DNAD07_Rottweiler


title: WG0087816-DNAD01_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAB06_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAC06_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAE05_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAB03_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAB05_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAD02_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAA06_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAB04_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAB02_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAA04_Nova Scotia Duck Tolling Retriever


title: WG0087816-DNAB01_Nova Scotia Duck Tolling Retriever


title: WG0093353-DNAB08_New Foundland

value: New Foundland


title: WG0093353-DNAA09_Mops

value: Mops


title: WG0087816-DNAA01_Nova Scotia Duck Tolling Retriever

value: blood


title: WG0087816-DNAA03_Nova Scotia Duck Tolling Retriever


title: WG0093353-DNAD09_Labrador Retriever

value: Labrador Retriever


title: WG0087816-DNAA02_Nova Scotia Duck Tolling Retriever


title: LAB028_Labrador Retriever


title: LAB031_Labrador Retriever


title: WG0087816-DNAG06_Large Munsterlander

value: Large Munsterlander


title: LAB019_Labrador Retriever


title: LAB010_Labrador Retriever


title: LAB012_Labrador Retriever


title: LAB020_Labrador Retriever


title: WG0093353-DNAC09_Labrador Retriever


title: WG0087816-DNAE06_Jack Russell Terrier

value: Jack Russell Terrier


title: WG0093353-DNAH08_Mops


title: LAB026_Labrador Retriever


title: LAB017_Labrador Retriever


title: WG0087816-DNAF06_Jack Russell Terrier


title: LAB021_Labrador Retriever


title: JRT030_Jack Russell Terrier


title: WG0093353-DNAC08_New Foundland


title: LAB016_Labrador Retriever


title: JRT017_Jack Russell Terrier


title: LAB011_Labrador Retriever


title: LAB005_Labrador Retriever


title: JRT022_Jack Russell Terrier


title: JRT018_Jack Russell Terrier


title: JRT001_Jack Russell Terrier


title: GRY032_Greyhound

value: Greyhound


title: JRT026_Jack Russell Terrier


title: JRT005_Jack Russell Terrier


title: JRT002_Jack Russell Terrier


title: GRY019_Greyhound


title: JRT013_Jack Russell Terrier


title: GRY014_Greyhound


title: JRT014_Jack Russell Terrier


title: GRY029_Greyhound


title: GRY002_Greyhound


title: GRY008_Greyhound


title: GRY005_Greyhound


title: GRY015_Greyhound


title: GRY004_Greyhound


title: GRY020_Greyhound


title: WG0093353-DNAG06_Greenland sledge dog

value: Greenland sledge dog


title: WG0093353-DNAH06_Greenland sledge dog

value: Male


title: WG0093353-DNAE07_Greenland sledge dog


title: WG0093353-DNAF06_Greenland sledge dog


title: WG0093353-DNAB07_Greenland sledge dog


title: GRY022_Greyhound


title: WG0093353-DNAF07_Greenland sledge dog


title: WG0093353-DNAC06_Greenland sledge dog


title: WG0093353-DNAD06_Greenland sledge dog


title: WG0093353-DNAD07_Greenland sledge dog


title: WG0093353-DNAC07_Greenland sledge dog


title: WG0093353-DNAE06_Greenland sledge dog


title: WG0093352-DNAF11_Golden Retriever

value: Golden Retriever


title: WG0093353-DNAA07_Greenland sledge dog


title: WG0093352-DNAC12_Golden Retriever


title: WG0093352-DNAH11_Golden Retriever


title: HUVEC treated biological rep 3

city: Mannheim

first: Benito

middle: Antonio

last: Yard

address: Theodor-Kutzer-Ufer 1-3

department: Vth medical clinic

institute: University of Heidelberg

description: Gene expression data from NOD treated HUVEC

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of HGU133A_2 -type from Affymetrix. A Custom CDF Version 13 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: HUVEC treated at P3

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

growth_protocol: HUVECs were cultured in basal endothelial medium supplemented with 10% fetal bovine serum (FBS), essential growth factors and antibiotics

extract_protocol: Total RNA was isolated from HUVECs using Trizol®-Reagent. DNase treatment was carried out and RNA concentration and quality were assessed on a Bioanalyser 2100 system

treatment_protocol: HUVECs were treated with 100µM of NOD for 24 hrs or left untreated.

tag: cell line

value: HUVEC

value: 100µM of NOD for 24 hrs


title: HUVEC treated biological rep 1


title: HUVEC treated biological rep 2


title: HUVEC biological rep 1

description: Gene expression data from untreated HUVEC

source_name: HUVEC P3


title: WG0093353-DNAA01_Golden Retriever


title: WG0093352-DNAB11_Golden Retriever


title: WG0093352-DNAE11_Golden Retriever


title: HUVEC biological rep 2


title: WG0093352-DNAG10_Golden Retriever


title: GSD031_German Shepherd Dog

value: German Shepherd Dog


title: Verdejo_pericarp_2011/09/13_18:00h_rep1

city: Logrono

first: Pablo

last: Carbonell-Bejerano

state: La Rioja

address: Madre de Dios, 51

department: Instituto de las Ciencias de la Vid y del Vino

country: Spain

institute: CSIC

description:
V 2011/08/10 18:00h-1
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 18:00h. It is the first of three replicates for this time point, each from separate blocks.

hyb_protocol: If the quality control was correct, then 4 µg of labelled cDNA were hybridized. Hybridization solution (NimbleGen Hybridization kit) was added to each labelled cDNA and hybridization was performed for 16 h at 42ºC in a HS 4 Hybridization station (NimbleGen-Roche).

scan_protocol: Hybridized microarrays were washed with Wash buffer kit (NimbleGen-Roche) and scanned at 532 nm and 2 µm resolution in a DNA Microarray Scanner with Surescan High-Resolution Technology (Agilent technologies).

data_processing: After evaluation of hybridization quality by Experimental metrics report implemented in NimbleScan Software version 2.6 (NimbleGen-Roche), probeset signal values from all the microarray hybridizations were background corrected and normalized together using Robust Microarray Average (RMA) (Irizarry et al., 2003) in NimbleScan Software, which produces a calls file for each sample with normalized expression data for each gene.

organism: Vitis vinifera

label_protocol: cDNA was synthesized from 10 µg of total RNA using cDNA Synthesis System Kit (NimbleGen-Roche). The cDNA preparation (1 µg) was amplified and labelled with Cy3-random nonamers using One color labeling kit (NimbleGen-Roche).

growth_protocol:
Experiment using V. vinifera cv. Tempranillo was conducted with three years old potted plants, grafted on rootstock 110 Richter. Soil inside pots (50•45•40 cm) was composed buy a peat:sand:vegetal sand mix (63:25:12) over a 5 cm stones layer at the bottom. Tempranillo plants were housed in an experimental greenhouse from Bodegas Miguel Torres S.L. located in Pacs del Penedès (Catalonia, northeast Spain). Greenhouse was roof-covered with glass allowing for sunlight transmission and no other light was supplied. Pots were covered with white plastic films and dropper irrigated according to plant requirements that were calculated as: Week water supply = WU * PET * Watering coefficient (WU, water use by plants in the previous week; PET, potential evapotranspiration; Watering coefficient, 90%). WU was calculated by using weighing lysimeters. Temperature inside the chamber was regulated by Exafan coolers (Grup Sabater, Argentona, Spain) to be the same as external ambient temperature. Temperature and humidity inside the camera were registered each 10 min by MCU Clima sensors (Grup Sabater). Vines were pruned during the vegetative phase and apexes were removed throughout the ripening season.
Experiment using V. vinifera cv. Verdejo was conducted with five years old vines from a grapevine cultivars collection garden belonging to Bodegas Matarromera S.L. located in Valbuena de Duero (Valladolid, Castilla y León, central plateau Spain). Verdejo vines grafted on 110 Richter rootstocks were conducted in a driving trellis system, in a row orientated in E-W direction. The Verdejo vineyard was dropper irrigated in two different days during the ripening season (2 L•h-1) and defoliation practises were not carried out. Three blocks of ten plants in the same row separated by other ten plants in between were delimited as replicates for the Verdejo experiment.

extract_protocol: Tempranillo and Verdejo frozen berries were peeled and de-seeded, respectively. About 10-15 berries were used for RNA extraction on each sample. Total RNA was extracted from frozen Tempranillo berry skin and Verdejo pericarp as described by Reid et al. (Reid et al., 2006). DNase digestion of contaminating DNA in the RNA samples was carried out with the RNase-Free DNase Set (QIAGEN). Final RNA purification was carried out using the SpektrumTM Plant Total RNA kit (Sigma-Aldrich) according to standard protocols.

tag: cultivar

value: Verdejo

value: Pericarp

tag: tissue cpllection date&time


title: Verdejo_pericarp_2011/09/13_13:45h_rep3

description:
V 2011/08/10 13:45h-3
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 13:45h. It is the third of three replicates for this time point, each from separate blocks.


title: Verdejo_pericarp_2011/09/13_18:00h_rep2

description:
V 2011/08/10 18:00h-2
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 18:00h. It is the second of three replicates for this time point, each from separate blocks.


title: GSD029_German Shepherd Dog


title: GSD019_German Shepherd Dog


title: Verdejo_pericarp_2011/09/13_13:45h_rep2

description:
V 2011/08/10 13:45h-2
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 13:45h. It is the second of three replicates for this time point, each from separate blocks.


title: Verdejo_pericarp_2011/09/13_13:45h_rep1

description:
V 2011/08/10 13:45h-1
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 13:45h. It is the first of three replicates for this time point, each from separate blocks.


title: GSD024_German Shepherd Dog


title: WG0093352-DNAH10_Golden Retriever


title: Verdejo_pericarp_2011/09/13_18:00h_rep3

description:
V 2011/08/10 18:00h-3
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 18:00h. It is the third of three replicates for this time point, each from separate blocks.


title: WG0093351-DNAA01_Golden Retriever


title: WG0093352-DNAA11_Golden Retriever


title: Verdejo_pericarp_2011/09/13_8:45h_rep3

description:
V 2011/08/10 8:45h-3
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 8:45h. It is the third of three replicates for this time point, each from separate blocks.


title: WG0093352-DNAA12_Golden Retriever


title: GSD014_German Shepherd Dog


title: WG0093352-DNAB12_Golden Retriever


title: Verdejo_pericarp_2011/09/13_8:45h_rep2

description:
V 2011/08/10 8:45h-2
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 8:45h. It is the second of three replicates for this time point, each from separate blocks.


title: Verdejo_pericarp_2011/09/13_4:30h_rep3

description:
V 2011/08/10 4:30h-3
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 4:45h. It is the third of three replicates for this time point, each from separate blocks.


title: Verdejo_pericarp_2011/09/12_23:45h_rep1

description:
V 2011/08/09 23:45h-1
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 23:45h. It is the first of three replicates for this time point, each from separate blocks.


title: Verdejo_pericarp_2011/09/13_4:30h_rep2

description:
V 2011/08/10 4:30h-2
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 4:45h. It is the second of three replicates for this time point, each from separate blocks.


title: Verdejo_pericarp_2011/09/12_23:45h_rep3

description:
V 2011/08/09 23:45h-3
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 23:45h. It is the third of three replicates for this time point, each from separate blocks.


title: Verdejo_pericarp_2011/09/13_4:30h_rep1

description:
V 2011/08/10 4:30h-1
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 4:45h. It is the first of three replicates for this time point, each from separate blocks.


title: GSD008_German Shepherd Dog


title: GSD017_German Shepherd Dog


title: WG0093353-DNAH02_Finnish Spitz

value: Finnish Spitz


title: Verdejo_pericarp_2011/09/12_23:45h_rep2

description:
V 2011/08/09 23:45h-2
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 23:45h. It is the second of three replicates for this time point, each from separate blocks.


title: WG0093353-DNAH07_Flatcoated Retriever

value: Flatcoated Retriever


title: GSD004_German Shepherd Dog


title: WG0093353-DNAG07_Flatcoated Retriever

value: Female


title: WG0093353-DNAG02_Finnish Spitz


title: GSD012_German Shepherd Dog


title: Verdejo_pericarp_2011/09/12_19:30h_rep2

description:
V 2011/08/09 19:30h-2
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/12 19:30h. It is the second of three replicates for this time point, each from separate blocks.


title: GSD007_German Shepherd Dog


title: Verdejo_pericarp_2011/09/12_19:30h_rep3

description:
V 2011/08/09 19:30h-3
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/12 19:30h. It is the third of three replicates for this time point, each from separate blocks.


title: Verdejo_pericarp_2011/09/12_19:30h_rep1

description:
V 2011/08/09 19:30h-1
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/12 19:30h. It is the first of three replicates for this time point, each from separate blocks.


title: WG0093353-DNAF03_Finnish Spitz


title: Verdejo_pericarp_2011/09/13_8:45h_rep1

description:
V 2011/08/10 8:45h-1
This sample is of Vitis vinifera cv. Verdejo pericarp collected at 2011/09/13 8:45h. It is the first of three replicates for this time point, each from separate blocks.


title: WG0093353-DNAF02_Finnish Spitz


title: Tempranillo_flesh_2011/08/10_18:00h_rep2

description:
F 2011/08/10 18:00h-2
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 18:00h. It is the second of three replicates for this time point, each from separate blocks.

value: Tempranillo

value: Berry flesh


title: Tempranillo_flesh_2011/08/10_18:00h_rep3

description:
F 2011/08/10 18:00h-3
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 18:00h. It is the third of three replicates for this time point, each from separate blocks.


title: Tempranillo_flesh_2011/08/10_18:00h_rep1

description:
F 2011/08/10 18:00h-1
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 18:00h. It is the first of three replicates for this time point, each from separate blocks.


title: WG0093353-DNAE03_Finnish Spitz

value: blood


title: WG0093353-DNAE02_Finnish Spitz


title: Tempranillo_flesh_2011/08/10_12:45h_rep2

description:
F 2011/08/10 12:45h-2
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 12:45h. It is the second of three replicates for this time point, each from separate blocks.


title: WG0093353-DNAC02_Finnish Spitz


title: Tempranillo_flesh_2011/08/10_12:45h_rep3

description:
F 2011/08/10 12:45h-3
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 12:45h. It is the third of three replicates for this time point, each from separate blocks.


title: WG0093353-DNAB03_Finnish Spitz


title: WG0093353-DNAD02_Finnish Spitz


title: WG0093353-DNAC03_Finnish Spitz


title: WG0093353-DNAH05_Eurasian

value: Eurasian


title: Tempranillo_flesh_2011/08/10_4:00h_rep3

description:
F 2011/08/10 4:00h-3
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 4:00h. It is the third of three replicates for this time point, each from separate blocks.


title: Tempranillo_flesh_2011/08/10_7:45h_rep1

description:
F 2011/08/10 7:45h-1
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 7:45h. It is the first of three replicates for this time point, each from separate blocks.


title: Tempranillo_flesh_2011/08/10_12:45h_rep1

description:
F 2011/08/10 12:45h-1
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 12:45h. It is the first of three replicates for this time point, each from separate blocks.


title: Tempranillo_flesh_2011/08/10_7:45h_rep3

description:
F 2011/08/10 7:45h-3
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 7:45h. It is the third of three replicates for this time point, each from separate blocks.


title: WG0093353-DNAD03_Finnish Spitz


title: Tempranillo_flesh_2011/08/10_4:00h_rep1

description:
F 2011/08/10 4:00h-1
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 4:00h. It is the first of three replicates for this time point, each from separate blocks.


title: WG0093353-DNAH04_Eurasian


title: Tempranillo_flesh_2011/08/10_4:00h_rep2

description:
F 2011/08/10 4:00h-2
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 4:00h. It is the second of three replicates for this time point, each from separate blocks.


title: Tempranillo_flesh_2011/08/09_23:30h_rep2

description:
F 2011/08/09 23:30h-2
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 23:30h. It is the second of three replicates for this time point, each from separate blocks.


title: Tempranillo_flesh_2011/08/09_23:30h_rep1

description:
F 2011/08/09 23:30h-1
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 23:30h. It is the first of three replicates for this time point, each from separate blocks.


title: Tempranillo_flesh_2011/08/09_18:00h_rep3

description:
F 2011/08/09 18:00h-3
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/09 18:00h. It is the third of three replicates for this time point, each from separate blocks.


title: Tempranillo_flesh_2011/08/09_23:30h_rep3

description:
F 2011/08/09 23:30h-3
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 23:30h. It is the third of three replicates for this time point, each from separate blocks.


title: Tempranillo_flesh_2011/08/09_18:00h_rep1

description:
F 2011/08/09 18:00h-1
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/09 18:00h. It is the first of three replicates for this time point, each from separate blocks.


title: Tempranillo_flesh_2011/08/09_18:00h_rep2

description:
F 2011/08/09 18:00h-2
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/09 18:00h. It is the second of three replicates for this time point, each from separate blocks.


title: WG0093353-DNAB05_Eurasian


title: WG0093353-DNAD05_Eurasian


title: WG0093353-DNAE04_Eurasian


title: Tempranillo_skin_2011/08/10_18:00h_rep3

description:
S 2011/08/10 18:00h-3
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 18:00h. It is the third of three replicates for this time point, each from separate blocks.

value: Berry skin


title: WG0093353-DNAA03_Finnish Spitz


title: Tempranillo_flesh_2011/08/10_7:45h_rep2

description:
F 2011/08/10 7:45h-2
This sample is of Vitis vinifera cv. Tempranillo berry flesh collected at 2011/08/10 7:45h. It is the second of three replicates for this time point, each from separate blocks.


title: WG0093353-DNAF04_Eurasian


title: WG0093353-DNAA05_Eurasian


title: Tempranillo_skin_2011/08/10_18:00h_rep2

description:
S 2011/08/10 18:00h-2
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 18:00h. It is the second of three replicates for this time point, each from separate blocks.


title: WG0093351-DNAF10_English Setter

value: English Setter


title: WG0093353-DNAE05_Eurasian


title: WG0093353-DNAG04_Eurasian


title: GSD023_German Shepherd Dog


title: Tempranillo_skin_2011/08/10_12:45h_rep2

description:
S 2011/08/10 12:45h-2
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 12:45h. It is the second of three replicates for this time point, each from separate blocks.


title: Tempranillo_skin_2011/08/10_12:45h_rep3

description:
S 2011/08/10 12:45h-3
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 12:45h. It is the third of three replicates for this time point, each from separate blocks.


title: WG0093353-DNAG05_Eurasian


title: WG0093351-DNAG09_English Setter


title: WG0093351-DNAD10_English Setter


title: WG0093353-DNAC05_Eurasian


title: WG0093351-DNAE09_English Setter


title: Tempranillo_skin_2011/08/10_7:45h_rep3

description:
S 2011/08/10 7:45h-3
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 7:45h. It is the third of three replicates for this time point, each from separate blocks.


title: WG0093351-DNAC09_English Setter


title: Tempranillo_skin_2011/08/10_7:45h_rep2

description:
S 2011/08/10 7:45h-2
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 7:45h. It is the second of three replicates for this time point, each from separate blocks.


title: Tempranillo_skin_2011/08/10_18:00h_rep1

description:
S 2011/08/10 18:00h-1
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 18:00h. It is the first of three replicates for this time point, each from separate blocks.


title: WG0093351-DNAB09_English Setter


title: WG0093351-DNAE10_English Setter


title: Tempranillo_skin_2011/08/10_7:45h_rep1

description:
S 2011/08/10 7:45h-1
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 7:45h. It is the first of three replicates for this time point, each from separate blocks.


title: WG0093351-DNAB10_English Setter


title: WG0093351-DNAH09_English Setter


title: Tempranillo_skin_2011/08/10_12:45h_rep1

description:
S 2011/08/10 12:45h-1
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 12:45h. It is the first of three replicates for this time point, each from separate blocks.


title: WG0093351-DNAC10_English Setter


title: Tempranillo_skin_2011/08/09_23:30h_rep3

description:
S 2011/08/09 23:30h-3
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 23:30h. It is the third of three replicates for this time point, each from separate blocks.


title: Tempranillo_skin_2011/08/10_4:00h_rep1

description:
S 2011/08/10 4:00h-1
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 4:00h. It is the first of three replicates for this time point, each from separate blocks.


title: Tempranillo_skin_2011/08/10_4:00h_rep3

description:
S 2011/08/10 4:00h-3
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 4:00h. It is the third of three replicates for this time point, each from separate blocks.


title: Tempranillo_skin_2011/08/09_23:30h_rep1

description:
S 2011/08/09 23:30h-1
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 23:30h. It is the first of three replicates for this time point, each from separate blocks.


title: Tempranillo_skin_2011/08/09_23:30h_rep2

description:
S 2011/08/09 23:30h-2
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 23:30h. It is the second of three replicates for this time point, each from separate blocks.


title: Tempranillo_skin_2011/08/10_4:00h_rep2

description:
S 2011/08/10 4:00h-2
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/10 4:00h. It is the second of three replicates for this time point, each from separate blocks.


title: Tempranillo_skin_2011/08/09_18:00h_rep1

description:
S 2011/08/09 18:00h-1
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/09 18:00h. It is the first of three replicates for this time point, each from separate blocks.


title: WG0093351-DNAA10_English Setter


title: Tempranillo_skin_2011/08/09_18:00h_rep2

description:
S 2011/08/09 18:00h-2
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/09 18:00h. It is the second of three replicates for this time point, each from separate blocks.


title: Tempranillo_skin_2011/08/09_18:00h_rep3

description:
S 2011/08/09 18:00h-3
This sample is of Vitis vinifera cv. Tempranillo berry skin collected at 2011/08/09 18:00h. It is the third of three replicates for this time point, each from separate blocks.


title: WG0093351-DNAF04_English bulldog

value: English bulldog


title: WG0093351-DNAH05_English bulldog


title: WG0093351-DNAH04_English bulldog

value: Male


title: D3_C1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: iPS cells from PBMC

label_protocol: First strand cDNA synthesis was performed using a iScript cDNA synthesis kit  (Bio-Rad). Quantitative PCR analyses were performed using the CXF384 Realtime System  (Bio-Rad) and KAPA SYBR FAST qPCR Master Mix (2X) (KK4602).  pellets was performed for RNA isolation. RNA clean up was performed using a QIAGEN  RNeasy Kit. First strand cDNA synthesis was performed using a iScript cDNA synthesis kit  (Bio-Rad). Quantitative PCR analyses were performed using the CXF384 Realtime System  (Bio-Rad) and KAPA SYBR FAST qPCR Master Mix (2X) (KK4602).

extract_protocol: Direct application of PureZol (Bio-rad) onto adherent cells or cell  pellets was performed for RNA isolation. RNA clean up was performed using a QIAGEN  RNeasy Kit.

tag: cell type

value: iPS cells from PBMC


title: WG0093351-DNAG04_English bulldog


title: WG0093351-DNAD09_English Setter


title: C2_C2


title: liver_MASM+6.5Gy_rep4

city: ShangHai

first: Jian-Zhong

address: Guo He Road 325#

institute: Second Military Medical University

description: Gene expression after 24hr in 6.5Gy-irradiated rat liver pre-treated with MASM

hyb_protocol: The 4×44K Whole Rat Genome Oligo Microarray (Agilent technologies, Santa Clara, CA, US) was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions.After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Raw data were obtained by Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) and normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label_protocol: The total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted from the liver tissue of rat using TRIZOL Reagent (Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (QIAGEN, GmBH, Germany) and RNase-Free DNase Set (QIAGEN, GmBH, Germany).

treatment_protocol: The rats were randomly assigned to one of the three following treatment groups (10-12 animals per group): normal control, radiation and MASM dose (30 mg/kg body weight/day) + radiation. MASM dissolved in double distilled water were administered intragastrically to the male animals for 3 consecutive days before irradiation. Radiation was delivered by the 60Co source. Radiation doses were 6.5 Gy at a rate 2 Gy/min.

value: liver

value: male


title: WG0093351-DNAE04_English bulldog


title: D1_C2


title: liver_MASM+6.5Gy_rep3


title: D1_C1


title: D1_C3_250


title: liver_MASM+6.5Gy_rep1


title: WG0093351-DNAD04_English bulldog


title: WG0093351-DNAE05_English bulldog


title: liver_6.5Gy_rep3

description: Gene expression after 24hr in 6.5Gy-irradiated rat liver


title: WG0093351-DNAB05_English bulldog


title: liver_MASM+6.5Gy_rep2


title: WG0093353-DNAG01_Elkhound

value: Elkhound


title: F1 hybrid 454

tag: genotype

value: Arabidopsis thaliana x Arabidopsis lyrata hybrid

value: leaf


title: WG0093351-DNAA06_English bulldog


title: WG0093351-DNAD05_English bulldog


title: H7

source_name: hES cells

value: hES cells


title: WG0093353-DNAD01_Elkhound


title: WG0093353-DNAH01_Elkhound


title: WG0093353-DNAE01_Elkhound


title: WG0093351-DNAA05_English bulldog


title: liver_6.5Gy_rep2


title: WG0093353-DNAC01_Elkhound


title: liver_6.5Gy_rep1


title: liver_0Gy_rep2

description: Gene expression after 24hr in 0Gy-irradiated rat liver


title: WG0093353-DNAB01_Elkhound


title: D2_PBMC

source_name: peripheral blood mononucleated cell

value: peripheral blood mononucleated cell


title: H1


title: A. thaliana 454

organism: Arabidopsis thaliana


title: CHB8-1 [genex]

description: Gene expression data obtained from Human embryonic stem cells

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix U133 Plus 2.0 array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: RMA

source_name: Human ESC replicate1

label_protocol: Preparation of biotinylated cDNA was performed according to the standard Nugen amplification sample preparation protocol, starting with 100ng of total RNA

growth_protocol: standard HESC growth conditions as described in Pick et al. (2009).

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications

value: control

value: embryonic stem cell


title: CHB8-2 [genex]

source_name: Human ESC replicate2


title: D2_PBMC_D10


title: liver_0Gy_rep3


title: H9


title: WG0093352-DNAF12_Elkhound

value: Female


title: D1_PBMC


title: hFib2-2 [genex]

description: Gene expression data obtained from Normal Human fibroblast

source_name: Human normal Fibroblast replicate2

growth_protocol: Fibroblasts were grown in alpha-MEM containing 10 % inactivated fetal serum (IFS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM L-glutamine. Replacement,10 ng/ml bFGF, 1 mM L-glutamine, 100 uM nonessential amino acids, 100 uM 2-mercaptoethanol, 50 U/ml penicillin, and 50 mg/ml streptomycin).

value: normal

value: fibroblast


title: H2-1-p9-2 [genex]

description: Gene expression data obtained from iPS cells derived from Normal Human fibroblast

source_name: hFib2 normal iPSC passage9 replicate2

growth_protocol: For feeder-free culture of iPSCs, the plate was coated with 0.3mg/ml Matrigel (BD-Bioscience, San Jose, CA) and mTeSR (StemCell Technologies, Vancouver, Canada) was used according to the manufacturer’s instruction.

value: iPS cell (fibroblast-derived)


title: H2-1-p9-1 [genex]

source_name: hFib2 normal iPSC passage9 replicate1


title: WG0093352-DNAG12_Elkhound

value: blood


title: liver_0Gy_rep1


title: WG0093352-DNAE12_Elkhound


title: WG0093352-DNAD12_Elkhound


title: WG0093353-DNAF01_Elkhound


title: hFib2-1 [genex]

source_name: Human normal Fibroblast replicate1


title: WG0093351-DNAG05_English bulldog

value: English bulldog


title: K-rasG12Dint +HFD, rep2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

hyb_protocol: Biotinylated fragmented ssDNA was hybridized onto the GeneChip® Mouse Gene 1.0 ST Array (Affymetrix) according to the manufacturer's recommendation. The hybridization was performed for 16 h at 45°C in the GeneChip® Hybridization Oven 640 (Affymetrix). Washing and staining of the arrays were done on the GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer's recommendation.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: Data were quantile normalized and log2 transformed using R and Bioconductor package limma.

source_name: duodenum, K-rasG12Dint, HFD

label_protocol: For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. 0.3 µg of total RNA was used as start Material. The labeling reaction was performed by using the GeneChip® WT PLUS Reagent Kit from Affymetrix (Cat N° 902281) following manufacturer's instructions.

growth_protocol: Animals were housed at pathogen-free facility, under 12 hours dark/light cycle.

extract_protocol: Tissue samples were homogenized in Trizol buffer and mRNA was isolated in a single-step acid guanidinium thiocyanate-phenol-chloroform extraction following manufacturer's instructions (http://tools.invitrogen.com/content/sfs/manuals/trizol_reagent.pdf). RNA-precipitation was done with ethanol. RNA was diluted in nuclease-free water and concentrations were determined using a Nanodrop spectrophotometer.

treatment_protocol: Mice were euthanized with carbon dioxide inhalation.

value: C57BL/6J mix

tag: age

value: 8 months

tag: Sex

value: female

value: duodenum

value: high-fat diet


title: K-rasG12Dint +HFD, rep3

tag: treatment


title: WG0093352-DNAH12_Elkhound

source_name: blood

value: Elkhound


title: K-rasG12Dint +HFD, rep1


title: U87MG-SC10

city: La Jolla

first: Olivier

last: Harismendy

state: California

address: 3855 Health Sciences Drive #0820

department: Medicine / Moores Cancer Center

institute: UC San Diego

description: Hybridized to 250K_Nsp

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The ten sample .CEL files were analyzed using Genotyping Console Version 4.1.3.840 (Affymetrix). As suggested by the manufacturer, we analyzed the samples along with forty additional samples downloaded from the manufacturer’s website (39 HapMap and 1 non-HapMap sample) for accurate genotype calling in BRLMM algorithms. Genotype calling with BRLMM was performed on the Genotyping Console

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: The lines were propagated in standard serum-supplemented media consisting of DMEM (Life Technologies, Grand Island, NY) + 15% fetal bovine serum (FBS) (Sigma-Aldrich, St. Louis, MO) + 100 U/ml penicillin/100 ng/ml streptomycin (Life Technologies) in tissue culture treated plates at 37°C in humidified 5% CO2. Signle clones were derived and propagated in the same conditions.

extract_protocol: Genomic DNA was extracted using DNA extraction kit (Qiagen)

tag: cell line background

value: Glioblastoma

tag: subclone id


title: U87MG-SC11

description: Hybridized to 250K_Nsp


title: U87MG-SC9

description: Hybridized to 250K_Nsp


title: WG0087816-DNAH08_Dalmatian

value: Dalmatian


title: WG0087816-DNAF09_Dalmatian

value: Male


title: U87MG-SC8

description: Hybridized to 250K_Nsp


title: WG0087816-DNAD09_Dalmatian


title: U87MG-SC12

description: Hybridized to 250K_Nsp


title: U87MG-SC5

description: Hybridized to 250K_Nsp


title: LSL-K-rasG12D/+ +HFD, rep3

source_name: duodenum, LSL-K-rasG12D/+, HFD

tag: strain/background

tag: genotype/variation


title: WG0087816-DNAC09_Dalmatian

tag: breed


title: U87MG-SC3

description: Hybridized to 250K_Nsp


title: U87MG-SC6

description: Hybridized to 250K_Nsp


title: LSL-K-rasG12D/+ +HFD, rep1


title: WG0087816-DNAA09_Dalmatian


title: SIRT4 KO liver_7245

first: Gaelle

last: Laurent

address: 250 Longwood Avenue

department: Cell Biology

description: Gene expression from Ko liver

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array Mouse430_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Robust Multi-array Average (RMA) with PM only models as normalization method.

source_name: SIRT4 KO mouse liver after 16 hrs fast

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

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer instructions (Invitrogen). RNA was cleaned using RNeasy MiniKit from Qiagen.

treatment_protocol: No treatment. Samples are from SIRT4 WT or KO littermate mice on a 129 background.

tag: strain

value: male

value: SIRT4 KO

value: liver


title: SIRT4 KO liver_7581-2

description: Gene expression from Ko liver


title: WG0087816-DNAE09_Dalmatian

value: Female


title: WG0087816-DNAB09_Dalmatian


title: U87MG-SC2

description: Hybridized to 250K_Nsp


title: U87MG-SC1

description: Hybridized to 250K_Nsp


title: DCH031_Dachshund

value: Dachshund


title: K-rasG12Dint +ND, rep3

source_name: duodenum, K-rasG12Dint, ND

value: normal diet


title: K-rasG12Dint +ND, rep2


title: DCH029_Dachshund

value: blood


title: K-rasG12Dint +ND, rep1


title: LSL-K-rasG12D/+ +ND, rep3

source_name: duodenum, LSL-K-rasG12D/+, ND


title: LSL-K-rasG12D/+ +ND, rep2


title: SIRT4 KO liver_7235

description: Gene expression from Ko liver


title: SIRT4 KO liver_7211-2

description: Gene expression from Ko liver


title: SIRT4 KO liver_7236-2

description: Gene expression from Ko liver


title: SIRT4 KO liver_7232

description: Gene expression from Ko liver


title: DCH025_Dachshund


title: DCH027_Dachshund


title: LSL-K-rasG12D/+ +ND, rep1


title: K-rasG12Dint +HFD+Butyrate, rep3

source_name: duodenum, K-rasG12Dint, HFD + butyrate

value: 10 months

value: high-fat diet + butyrate


title: SIRT4 WT liver_7591

description: Gene expression from wt liver

source_name: WT mouse liver after 16 hrs fast

value: SIRT4 WT


title: LSL-K-rasG12D/+ +HFD, rep2

value: C57BL/6J mix

value: 8 months

value: female


title: SIRT4 WT liver_7587

description: Gene expression from wt liver


title: SIRT4 WT liver_7583

description: Gene expression from wt liver


title: DCH020_Dachshund


title: DCH022_Dachshund


title: K-rasG12Dint +HFD+Butyrate, rep2

value: duodenum


title: Replication timing of H2-1 iPSC, average of 2 biological replicates [CNV]

description:
submitted as of 2/24/14
H2-1_ave

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (34 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 1.1 kb across the human genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias, scaled to a reference data set to have the same median absolute deviation and averaged (limma package, R/Bioconductor).The mean early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

source_name: Early-replicating DNA of H2-1 iPSC cells

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

tag: diagnosis

tag: age (yrs)

value: M

tag: disease stage

tag: karyotype

value: iPS cell (fibroblast-derived)

tag: time

value: Early-replicating DNA

source_name: Late replicating DNA of H2-1 iPSC cells

value: Late-replicating DNA


title: SIRT4 WT liver_7244

description: Gene expression from wt liver

tag: gender

value: male

tag: tissue


title: K-rasG12Dint +HFD+Butyrate, rep1


title: SIRT4 WT liver_7577

description: Gene expression from wt liver

value: liver


title: Replication timing of BJ fibroblast, average of 2 biological replicates [CNV]

description:
submitted as of 2/24/14
BJ_ave

source_name: Early-replicating DNA of BJ fibroblast cells

value: newborn

tag: cell type

value: BJ fibroblast

source_name: Late replicating DNA of BJ fibroblast cells


title: Replication timing of hFib2 fibroblast, average of 2 biological replicates [CNV]

description:
submitted as of 2/24/14
hFib2_ave

source_name: Early-replicating DNA of hFib2 fibroblast cells

value: fibroblast

source_name: Late replicating DNA of hFib2 fibroblast cells


title: SIRT4 WT liver_7213

description: Gene expression from wt liver


title: LSL-K-rasG12D/+ +HFD+Butyrate, rep3

source_name: duodenum, LSL-K-rasG12D/+, HFD + butyrate

tag: age


title: LSL-K-rasG12D/+ +HFD+Butyrate, rep1

tag: Sex


title: DCH019_Dachshund

value: Dachshund

value: Female

value: blood


title: Mouse dermal fibroblast adam9 +/+, isolation 1

city: Charlottesville

first: Yongde

last: Bao

state: VA

department: MIC

institute: UVa

hyb_protocol: After labeling and cleaning, the fragmented cDNA were hybridized to Mouse Genome 430 2.0 GeneChips using the GeneChip Hybridization, Wash, and Stain Kit according to the manufacturer's manual.

scan_protocol: After hybridization at 48 C for 16 hours, the chips were scanned with an Affymetrix GeneChip Scanner 3000 7G. Data collection from there were packed into a tarball named XXX.DTT.

data_processing: Data out from the GeneChip system was checked for quality with Affymetrix Expression Console or in R-Bioconductor with appropriate packages. Subsequently, data were analyzed with both R-Bioconductor or dChip to cross-verify the findings.

source_name: fibroblasts isolated from mice skin at postnatal day 1, WT

label_protocol: The RNA samples were processed according to the protocols of 3' IVT Plus GeneChip Sample Preparation and Labeling kit.

growth_protocol: 1 million primary dermal fibroblasts from WT and adam9 KO animals were plated in a 10 cm square plate and cultured for 48 hours.

extract_protocol:
RNA was extracted with RNAzol according to the manufacturer's instructions.
All incoming RNA were checked to have good RIN. Tracking QC showed all meeting specs.

treatment_protocol: No treatment.

value: adam9 +/+

value: dermal fibroblasts

value: postnatal day 1


title: DCH010_Dachshund


title: Mouse dermal fibroblast adam9 +/+, isolation 2


title: DCH018_Dachshund

value: Male


title: wild type HDM, biological rep3

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

description: lung

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Gene-level intensity values for each of the chips were collected using Affymetrix Expression Console (EC) Software (Affymetrix, Santa Clara, CA).  The RMA-sketch workflow was applied for raw data preprocessing, which included global background correction, quantile normalization and median polish summarization.

source_name: wild-type, lung

label_protocol: 10 µg of sense strand cDNA was fragmented, labeled with biotin using terminal deoxynucleotidyl transferase.

growth_protocol: not applicable

extract_protocol: Biotin-labeled sense targets were prepared from samples of total lung RNA using the Affymetrix Whole-Transcript (WT) Sense Target Labeling Protocol without rRNA reduction.  Double-stranded cDNA templates were synthesized from 50 ng of total RNA using random hexamers coupled with a T7 promoter sequence and amplified by in vitro transcription (IVT) with T7 RNA polymerase to produce multiple copies of cRNAs.  Random hexamers were utilized to prepare sense strand cDNA.

treatment_protocol: Vldlr-/- mice and wild type (WT) B6129SF2/J mice received intranasal challenges of house dust mite (25 ucg) or saline, both in a volume of 10 ul, five days a week for 6 weeks.

value: lung

tag: genotype

value: wild-type


title: wild type HDM, biological rep4

description: lung


title: Mouse dermal fibroblast adam9 -/-, isolation 2

source_name: fibroblasts isolated from mice skin at postnatal day 1, adam9 KO

value: adam9 -/-


title: wild type HDM, biological rep2

description: lung


title: DCH007_Dachshund

source_name: blood


title: WG0093353-DNAE08_Cocker Spaniel

value: Cocker Spaniel


title: DCH017_Dachshund


title: DCH024_Dachshund


title: isolate23

city: Baltiomore

first: Christopher

last: Jacob

state: MD

address: 685 W. Baltimore St.

department: Center for Vaccine Development

institute: University of Maryland School of Medicine

hyb_protocol: described in Jacob et al, 2014

scan_protocol: Arrays were scanned on a NimbleGen MS 200 scanner using autogain setting per manufacturer's protocol (www.NimbleGen.com)

data_processing: data were processed by both a previously published method (PMCID: PMC3218861), and by a custom algorithm (Jacob et al, 2014, Submitted) (attached)

organism: Plasmodium falciparum

source_name: DNA from Southeast Asian Field Isolate

label_protocol: described in Jacob et al, 2014

extract_protocol: all samples were extracted using a Qiagen blood extraction mini prep (qiagen.com)

tag: origin

value: Field Isolate

tag: parasitemia (parasites/ul)

tag: leukocyte depletion status

value: Yes

tag: whole genome amplification status

value: No

tag: dna amount (qpcr determined) (ng)


title: isolate24


title: wild type HDM, biological rep1

description: lung

tag: strain


title: LSL-K-rasG12D/+ +HFD+Butyrate, rep2

tag: strain/background

value: C57BL/6J mix

tag: genotype/variation

value: 10 months

value: male

value: duodenum

tag: treatment

value: high-fat diet + butyrate


title: Mouse dermal fibroblast adam9 -/-, isolation 1


title: DFAT, Mkl1 siRNA transfection

city: Shinjuku-ku

first: Hiroyuki

last: NOBUSUE

state: Tokyo

address: 35 Shinanomachi

department: Institute for Advanced Medical Research

country: Japan

institute: Keio University School of Medicine

description: Gene expression data from DFAT cells transfected with Mkl1 siRNA

hyb_protocol: The Affymetrix GeneChip arrays were hybridized and washed using the manufacturer's protocol.

scan_protocol: Affymetrix GeneChip arrays were scanned using the Affymetrix GeneArray scanner.

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

source_name: DFAT, Mkl1 siRNA transfection

growth_protocol: DFAT cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% FBS in 5% CO2.

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

value: de-differentiated fat (DFAT)


title: WG0093351-DNAH11_Cocker spaniel

tag: breed

value: Cocker spaniel

value: Female

value: blood


title: isolate22


title: DFAT, Y-27632_treatment

description: Gene expression data from DFAT cells treated with Y-27632

source_name: DFAT, Y-27632_treatment


title: WG0093353-DNAF08_Cocker Spaniel

value: Male


title: Vldlr knockout HDM, biological rep4

description: lung

source_name: knock out, lung

value: lung

value: knock out


title: WG0093351-DNAF11_Cocker spaniel


title: Vldlr knockout HDM, biological rep3

description: lung


title: WG0093351-DNAH10_Cocker spaniel


title: Vldlr knockout HDM, biological rep1

description: lung


title: isolate20


title: isolate21


title: DFAT, Control siRNA transfection

description: Gene expression data from DFAT cells transfected with Control siRNA

source_name: DFAT, Control siRNA transfection


title: WG0093351-DNAE12_Cocker spaniel


title: isolate19


title: isolate18


title: Vldlr knockout HDM, biological rep2

description: lung


title: WG0093351-DNAD11_Cocker spaniel


title: Vldlr knockout saline, biological rep4

description: lung


title: WG0093351-DNAD12_Cocker spaniel


title: WG0093351-DNAE11_Cocker spaniel


title: isolate16


title: WG0093351-DNAG11_Cocker spaniel


title: isolate14


title: Vldlr knockout saline, biological rep1

description: lung


title: Vldlr knockout saline, biological rep3

description: lung


title: wild type saline, biological rep3

description: lung

value: wild-type


title: wild type saline, biological rep4

description: lung


title: wild type saline, biological rep2

description: lung


title: WG0093351-DNAA11_Cocker spaniel


title: isolate15


title: isolate12


title: isolate13


title: isolate11


title: DFAT, DMSO_treatment

description: Gene expression data from DFAT cells treated with DMSO

source_name: DFAT, DMSO_treatment


title: isolate10


title: Vldlr knockout saline, biological rep2

description: lung


title: WG0093351-DNAB12_Cocker spaniel


title: wild type saline, biological rep1

description: lung


title: isolate9


title: WG0093351-DNAB11_Cocker spaniel


title: WG0093351-DNAC12_Cocker spaniel


title: naïve bone marrow-GMP_rep3

city: Philadelphia

first: Mark

middle: C.

last: Siracusa

state: PA

address: 421 Curie Blvd

department: Microbiology

institute: UPenn

hyb_protocol: cDNA was amplied with NuGen WT Ovation Pico kit and hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST microarrays at the University of Pennsylvania’s Microarray facility.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Power Tools were used to process and quantile normalize fluorescent hybridization signals using Robust Multichip Averaging. Transcript values were log2 normalized.

source_name: bone marrow

label_protocol: Microarrays were washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

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

value: female

value: bone marrow

tag: tissue treatment

value: control-cDNA

value: GMP cells


title: WG0093351-DNAH01_Brittany Spaniels

value: Brittany Spaniels

tag: gender


title: isolate17

value: Field Isolate

value: Yes

value: No


title: naïve bone marrow-GMP_rep2

tag: tissue


title: WG0093351-DNAG01_Brittany Spaniels


title: naïve bone marrow-GMP_rep1

tag: cell type


title: isolate7


title: WG0093351-DNAF02_Brittany Spaniels


title: isolate6


title: WG0093351-DNAG02_Brittany Spaniels


title: isolate8


title: splenic TSLP-GMP_rep3

source_name: spleen

value: spleen

value: TSLP-cDNA

value: GMP-like cells


title: splenic TSLP-GMP_rep2


title: isolate5


title: WG0093351-DNAE02_Brittany Spaniels


title: splenic TSLP-GMP_rep1


title: WG0093351-DNAE01_Brittany Spaniels


title: isolate3


title: isolate4


title: WG0093351-DNAD02_Brittany Spaniels


title: LET_7C_2

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

institute: Goehte University Frankfurt

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CB-HSPCs, transduced with LeGO-let-7c, grown 7 days in megakarycytic differentiation medium, exp 2

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

growth_protocol: CB-HSPCs cells were grown in StemSpan, supplemented with SCF (1ng/ml), TPO (30ng/ml), IL-9 (13.5ng/ml), IL-6 (7.5ng/ml).

extract_protocol: Direct-zol™ RNA MiniPrep Kit (Zymo Research)

treatment_protocol: CB-HSPCs were transduced with the indicated virus.

tag: cell line

value: cord blood CD34+-hematopoietic stem and progenitor cells (CB-HSPCs)

tag: genotype/variation (vector)

tag: exp


title: MIR_99A-125B_2

source_name: CB-HSPCs, transduced with LeGO-miR-99a~125b-2, grown 7 days in megakarycytic differentiation medium, exp 2


title: MIR_125B_2

source_name: CB-HSPCs, transduced with LeGO-miR-125b-2, grown 7 days in megakarycytic differentiation medium, exp 2


title: isolate2

tag: origin