title: GM6

status: Public on Jun 13 2014

city: Beijing

first: Junjun

last: Ding

address: Haidian

institute: Tsinghua University

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 6

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

organism: uncultured soil microorganism

source_name: Soil microbes in Tibetan grasslands

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

growth_protocol: In August 2011, a total of 73 samples were cellected in the Shennonjia Mountain. At each site, twelve plots (20 m ×20 m) comprising typical vegetation and soil attributes were selected for sampling. At each plot, ten to fifteen soil cores at a depth of 0-10 cm were taken, mixed thoroughly and sieved with 2 mm mesh to remove roots and stones. Soil samples were kept on ice when transporting to laboratory, divided into two subsamples and stored at either 4°C for soil biogeochemical measurements or −80°C for DNA extraction.

extract_protocol: Soil DNA was extracted by freeze-grinding mechanical lysis as previously described (Zhou et al 1996). Freshly extracted DNA was purified twice using 0.5% low melting point agarose gel followed by phenol-chloroform-butanol extraction. DNA quality and quantity were assessed by the ratios of 260 nm/280 nm and 260 nm/230 nm, and final DNA contents were quantified with a PicoGreen method using a FLUO star Optima .

tag: elevation


title: GM12

type: genomic

country: China

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 12

molecule: genomic DNA

treatment_protocol: In August 2011, a total of 73 samples were cellected in the Shennonjia Mountain. At each site, twelve plots (20 m ×20 m) comprising typical vegetation and soil attributes were selected for sampling. At each plot, ten to fifteen soil cores at a depth of 0-10 cm were taken, mixed thoroughly and sieved with 2 mm mesh to remove roots and stones. Soil samples were kept on ice when transporting to laboratory, divided into two subsamples and stored at either 4°C for soil biogeochemical measurements or −80°C for DNA extraction.


title: GM15

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 15


title: GM7

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 7


title: GM5

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 5


title: GM3

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 3


title: GM4

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 4


title: GM10

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 10


title: GM9

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 9


title: GM13

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 13


title: GM8

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 8


title: GM11

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 11


title: GM1

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 1


title: LS13

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 13


title: LS15

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 15


title: GM2

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 2


title: LS12

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 12


title: GM14

description: GeoChip data for soil sample collected at the 2720-2776m elevation, replicate 14


title: LS14

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 14


title: LS9

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 9


title: LS10

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 10


title: LS7

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 7


title: LS4

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 4


title: LS6

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 6


title: LS3

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 3


title: LS2

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 2


title: LS11

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 11


title: LS5

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 5


title: LS8

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 8


title: HJ12

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 12


title: HJ9

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 9


title: HJ4

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 4


title: HJ7

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 7


title: HJ5

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 5


title: HJ13

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 13


title: HJ15

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 15


title: HJ6

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 6


title: JH15

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 15


title: HJ3

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 3


title: HJ1

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 1


title: HJ8

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 8


title: JH12

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 12


title: LS1

description: GeoChip data for soil sample collected at the 2456-2632m elevation, replicate 1


title: HJ10

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 10


title: HJ14

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 14


title: JH13

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 13


title: HJ11

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 11


title: JH14

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 14


title: HJ2

description: GeoChip data for soil sample collected at the 2243-2350m elevation, replicate 2


title: phc98021

status: Public on Jun 14 2014

type: RNA

city: Bethesda

first: Henry

middle: H

last: Zhang

state: MD

address: 49 Convent Drive

department: NICHD Bioinformatics and Scientific Programming Core

country: USA

institute: NICHD

description: Gene expresion data from sample phc98021

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 high resolution scanner (M10).

data_processing: The data were analyzed with the software of RMAExpress with custom CDF file, quantile normalization, background adjust, and median polish.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: liver tissue of subject 11, non-tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: tissue

value: liver


title: JH8

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 8


title: JH7

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 7


title: JH9

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 9


title: JH5

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 5


title: JH6

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 6


title: JH4

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 4


title: JH10

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 10


title: Liver_1_ZT02

type: SRA

city: Lausanne

first: Kyle

middle: Bergin

last: Gustafson

state: Suisse

address: EPFL-UPNAE

department: IBI

country: Switzerland

institute: EPFL

library_source: transcriptomic

data_processing:
RNA-seq mapping was performed with the STAR mapping protocol (Dobin et al. Bioinformatics 2013)
bam2wig.py at http://rseqc.sourceforge.net/
wigToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: WIG and BigWig standard

organism: Mus musculus

source_name: liver

growth_protocol: All animal studies were conducted in accordance with our regional committee for ethics in animal experimentation and the regulations of the veterinary office of the Canton of Vaud. C57Bl/6J mice were purchased from Janvier (Le Genest) or Charles River Laboratory. In all experiments, male mice between 10 and 12 wk of age are used. Unless noted otherwise, mice were maintained under standard animal housing conditions, with free access to food and water and in 12-h light/12-h dark cycles. However, for all experiments, animals were fed only at night during 4 d before the experiment to reduce effects of feeding rhythm.

extract_protocol:
Briefly, fractions were precipitated by the addition of three volumes of ethanol and kept overnight at 280uC. After 30 min of centrifugation at 5,200 g, RNAs were extracted from the non- soluble fraction by classical protocol
Liver RNAs were extracted and analysed by real-time quantitative RT-PCR, mostly as previously described [25]. Briefly, 0.5 mg of liver RNA was reverse transcribed using random hexamers and SuperScript II reverse transcriptase (Life Technol- ogies). The cDNAs equivalent to 20 ng of RNA were PCR amplified in triplicate in an ABI PRISM 7700 Sequence Detection System (Applied Biosystem) using the TaqMan or the SYBR Green technologies.

treatment_protocol: Livers were homogenized in lysis buffer containing 20 mM HEPES (pH 7.6), 250 mM NaCl, 10 mM MgCl2, 10 mM DTT, 20 mg/ml cycloheximid, 10 U/ml RNase inhibitor, and a protease inhibitor cocktail containing 0.5 mM PMSF, 10 mg/ml Aprotinin, 0.7 mg/ml Pepstatin A, and 0.7 mg/ml Leupeptin.

tag: strain

tag: age

tag: light/dark cycle

tag: water/food access


title: JH3

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 3


title: JH2

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 2


title: LK4

description: GeoChip data for soil sample collected at the 1715-1575m elevation, replicate 4


title: JC1

description: GeoChip data for soil sample collected at the 1059-1057m elevation, replicate 1


title: LK1

description: GeoChip data for soil sample collected at the 1715-1575m elevation, replicate 1


title: JC7

description: GeoChip data for soil sample collected at the 1059-1057m elevation, replicate 7


title: JH1

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 1


title: LK5

description: GeoChip data for soil sample collected at the 1715-1575m elevation, replicate 5


title: JC2

description: GeoChip data for soil sample collected at the 1059-1057m elevation, replicate 2


title: JC4

description: GeoChip data for soil sample collected at the 1059-1057m elevation, replicate 4


title: JC8

description: GeoChip data for soil sample collected at the 1059-1057m elevation, replicate 8


title: LK3

description: GeoChip data for soil sample collected at the 1715-1575m elevation, replicate 3


title: JC5

description: GeoChip data for soil sample collected at the 1059-1057m elevation, replicate 5


title: LK2

description: GeoChip data for soil sample collected at the 1715-1575m elevation, replicate 2


title: JC3

description: GeoChip data for soil sample collected at the 1059-1057m elevation, replicate 3


title: Fibroadenoma sample 007

city: Singapore

first: Weng Khong

last: Lim

state: Singapore

address: 11 Hospital Drive

department: Department of Medical Sciences

country: Singapore

institute: National Cancer Centre Singapore

description: Gene expression profiling of breast fibroadenomas

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G

data_processing: CEL files were loaded into R and then preprocessed and normalized using RMA. A custom CDF was used to reannotate the probes (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17.0.0/entrezg.asp).

source_name: Excised fibroadenoma tumor

label_protocol: Standard Affymetrix protocol, 10ug of RNAeasy-purified total RNA

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's instructions, followed by purification using the Qiagen RNAeasy kit.

tag: med12 status

value: Mutant


title: Fibroadenoma sample 005


title: BM-MTG16_WT

city: New York

first: Hiyaa

middle: Singhee

last: Ghosh

state: NY

address: 701 W 168th Street

institute: Columbia University Medical Center

hyb_protocol: Biotinylated DNA probe was made according to the standard Affymetrix protocol

scan_protocol: Arrays were scanned according to the Affymetrix protocol

data_processing: Affymetrix manufacturer software (employing gcRMA normalization) was used to process data.

source_name: Bone marrow

label_protocol: Used the Ambion WT labelling kit as per manufacturer's instructions using 200ng of starting total RNA

tag: cell type

value: dendritic cells

tag: genotype/variation

value: wild type


title: Fibroadenoma sample 009

value: Wild-type


title: Fibroadenoma sample 010


title: BM-MTG16_KO


title: JC6

description: GeoChip data for soil sample collected at the 1059-1057m elevation, replicate 6


title: Fibroadenoma sample 003


title: Fibroadenoma sample 012


title: Fibroadenoma sample 004


title: Fibroadenoma sample 006


title: Fibroadenoma sample 002


title: Fibroadenoma sample 011


title: Control_AF_5

city: Medford

first: Heather

middle: C

last: Wick

state: MA

address: 161 College Ave

department: Department of Computer Science

institute: Tufts University

description: gene expression data from 2nd trimester normal fetus

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.

source_name: AF cell free mRNA from 2nd trimester euploid fetus

label_protocol: Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)

extract_protocol: RNA was extracted from 5 ml AF supernatant with use of the QIAamp Circulating Nucleic Acid Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol under the section “Purification of circulating RNA from 5 ml serum or plasma” and as described in Dietz et al., 2011 [12].  Samples were stored at -80ºC until further analysis.

tag: fetal sex

value: female

tag: karyotype


title: Control_AF_3


title: Epithelia -/- 2

city: Bellinzona

first: Diletta

last: Di Mitri

state: Switzerland

address: Via Mirasole

institute: IOR-IOSI

hyb_protocol: 600ng of labeled specimens were hybridized on Agilent SurePrint G3 Mouse 8x60K Gene Expression arrays

scan_protocol: After 17 hours from hybridization, slides were washed and scanned using the Agilent Scanner version C (G2505C, Agilent Technologies).

data_processing: Images were analyzed using the Feature Extraction software v10.7. Raw data elaboration was carried out with Bioconductor (www.bioconductor.org), using R (v3.0.2) statistical language. Background correction was performed with the normexp method with an offset of 50 and quantile was used for between-array normalization. The LIMMA (LInear Models for Microarray Analysis) package was then used to identify differentially expressed genes, using the empirical Bayes method to compute a moderated t-statistics.

source_name: epithelial cells

label_protocol: Gene expression profiling was carried out using the one-color labeling method. Labeling, hybridization, washing and slide scanning were performed following the manufacturers protocols. Briefly, equal amounts of total RNA (100 ng) was amplified, labeled with Cy3 and purified with columns..

extract_protocol: Total RNA was isolated from epithelial and myeloid cell populations using miRNeasy Mini kit (Qiagen) following the manufacturer instructions and quantified by NanoDrop ND-1000 Spectro-photometer (NanoDrop Technologies, Wilming-ton, DE). RNA quality was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

treatment_protocol: Pten pc-/- 8 weeks old mice were sacrificed and whole prostates were isolated and processed to single cell suspension. Single cells were stained with specific anti-mouse monoclonal antibodies and cell-sorted using a FACSAria cell sorter (BD Biosciences).

value: 8 week old

value: epithelia


title: Control_AF_4


title: Turner_AF_3

description: gene expression data from 2nd trimester fetus with Turners

source_name: AF cell free mRNA from 2nd trimester Turners syndrome fetus


title: Epithelia -/- 1


title: Control_AF_1


title: Turner_AF_5


title: Myeloid-2

source_name: Gr-1+ myeloid cells

value: myeloid


title: Myeloid 1


title: Control_AF_2


title: Turner_AF_1


title: Gravi-stimulated at 30 min replicate 1

status: Public on Jun 12 2014

city: Nagoya

first: Miyo

middle: Terao

last: Morita

address: Furocho, Chikusa

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

description:
Biological replicate 1 of 2, Gravi-stimulated at 30 min
up_vs_low-30_rep1

hyb_protocol: Hybridized at 60°C for 17 hr. After hybridizetion, slides were washed sequential.

scan_protocol: Scanned on Agilent Technologies Microarray Scanner (resolution: 10µm)

data_processing: Extracted  features which fulfill the next confditions; ControlType=0, gIsSaturated=0, rIsSaturated=0, gIsPosAndSingnif=1, rIsPosAnd Singnif=1, gIsWellAvoveBG=1, rIsWellAvoveBG=1 and P value <0.01.

organism: Arabidopsis thaliana

source_name: Lower flanks at 30 min

label_protocol: 500 ng of total RNA was used for cDNA synthesis and cRNA labeling reaction with Agilent Low RNA Input Fluorescent Linear Amplification Kit. In this reaction, each cRNA was labeled both cyanine-3 and cyanine-5 in separate reactions.

growth_protocol: Seeds were sterilized and plated on Murashige and Skoog (MS) plates followed by treatment at 4°C for 3days. Seedlings were germinated under constant light at 23°C for 10 days. Plant were transplanted and grown on soil under constant white light at 23°C.

extract_protocol: Total RNA extracted using Rneasy Plant Mini kit (Qiagen) following manufacturer's instructions

treatment_protocol: To gravi-stimulate the inflorescence stems, plants harboring primary stems 4-8 cm in length were placed horizontally under non-directional dim light at 23°C. Gravi-stimulated stems were decapitated 5 mm from the top of inflorescences, and segments 3 cm in length from the cutting position were used. For preparing the sample of upper and lower flanks, these segments were sectioned longitudinally and manually.

tag: ecotype

value: Col

tag: treatment

value: gravi-stimulation

tag: time

value: 30 min

value: Inflorescence stems

tag: tissue segment

value: Lower flanks

source_name: Upper flanks at 30 min

value: Upper flanks


title: Gravi-stimulated at 10 min replicate 1

description:
Biological replicate 1 of 2, Gravi-stimulated at 10 min
up_vs_low-10_rep1

source_name: Lower flanks at 10 min

value: 10 min

source_name: Upper flanks at 10 min


title: Turner_AF_2


title: Turner_AF_4


title: Gravi-stimulated at 10 min replicate 2 (dye swapped)

description:
Biological replicate 2 of 2, Gravi-stimulated at 10 min
up_vs_low-10_rep2


title: Gravi-stimulated at 30 min replicate 2 (dye swapped)

description:
Biological replicate 2 of 2, Gravi-stimulated at 30 min
up_vs_low-30_rep2


title: LNCaP-control-2

city: Buffalo

first: Jianmin

last: Wang

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description: LNCaP cellline, androgen dependent, vector

hyb_protocol: 750 ng of labeled cRNA was hybridized to the HumanHT-12 v4 Expression BeadChip (Illumina, Cat# BD-103-0204) following manufacturer’s instructions

scan_protocol: Hybridized Beadchips were then scanned using the Illumina Iscan system

data_processing: Expression data are normalized using quantile normalization and differential expressed genes are identified using limma R package

source_name: LNCaP cell line

label_protocol: 500 ng of total RNA was labeled using the Illumina Total Prep Amplification Kit (Life Technologies, Cat.# AMIL1791) following manufacturer’s instructions.

growth_protocol: Prostate cancer cell lines LNCaP were cultured in RPMI 1640 media supplemented with 10% FBS and incubated at 37ºC in a humidified incubator containing 5% CO2.

extract_protocol: RNA was isolated from six samples: LNCaP shFOXO4 cell line, LNCaP pGIPZ control cell line, LNCaP shFOXO4 primary tumor, LNCaP pGIPZ control primary tumor, LNCaP shFOXO4 lymph node metastases and LNCaP pGIPZ control lymph node metastases. Total RNA from frozen cell pellets and tissues was prepared using Trizol (Invitrogen) following manufacturer’s instructions. Before labeling, RNA samples were quantitated using a ND-1000 spectrophotometer (NanoDrop) and evaluated for degradation using a 2100 Bioanalyzer (Agilent Technologies). Samples are required to have a RIN >7, an OD 260:280 of 1.9-2.0, and an OD 260/230 >1.8 for gene expression array analysis. Expression profiling was accomplished using the Human HT-12 whole-genome gene expression array and direct hybridization assay (Illumina, Inc.).

treatment_protocol: LNCaP cells were infected with lentiviruses (pGIPZ-GFP-FOXO4 shRNA or pGIPZ control shRNA) and shortly selected with puromycin. To generate the spontaneous metastasis model, these cell lines (2 X 105) will be orthotopically injected into the prostates of male athymic nude mice (Taconic Inc., Germantown, NY) in a total volume of 50 µl of sterile Matrigel using a 30-gauge needle.

value: human LNCAP cell line

tag: constuct

value: control


title: CaP-control-2

description: LNCaP prostate cancer, androgen-dependent, vector

source_name: orthotopic primary LNCaP tumor

value: human LNCAP tumor

tag: host organism

value: mouse


title: LNCaP-shFOXO4-2

description: LNCaP cellline, androgen dependent, shFOXO4 expressing


title: MetCaP-shFOXO4-1

description: LNCaP prostate cancer, lymph node metastasis, androgen-dependent, shFOXO4 expressing

source_name: LNCaP lymph node metastasis

value: human LNCAP tumor lymph node metastasis


title: CaP-control-1


title: MetCaP-shFOXO4-2

source_name: LNCaP cancer lymph node metastasis


title: MetCap-control-1

description: LNCaP prostate cancer, lymph node metastasis, androgen-dependent, vector


title: CaP-shFOXO4-1

description: LNCaP prostate cancer, androgen-dependent, shFOXO4 expressing


title: MetCap-control-2


title: CaP-shFOXO4-2

description: LNCaP prostate cancer, androgen-dependent. shFOXO4 expressing


title: LNCaP-control-1


title: JH11

description: GeoChip data for soil sample collected at the 1725-1844m elevation, replicate 11

source_name: Soil microbes in Tibetan grasslands

tag: elevation


title: LNCaP-shFOXO4-1

tag: tissue


title: NS08-609T-Xeno

city: Seoul

first: Young Taek

last: Oh

address: 50 Irwon-dong, Gangnam-gu

country: South Korea

institute: Samsung Medical Center

description: gene expression profile

hyb_protocol: Performed according to the manufacturer's (Affymetrix) recommendations.

data_processing: CEL files were normalized using Robust Multichip Averaging procedure.

source_name: patient 20

label_protocol: Biotinylated RNAs were prepared according to the manufacturer's recommendations.

extract_protocol: Total RNA was extracted according to the manufacturer’s recommendations.

value: Mus musculus

value: glioblastoma

tag: Stage

value: GBM (IV)


title: NS08-567T-Xeno

description: gene expression profile

scan_protocol: Performed according to the manufacturer's (Affymetrix) recommendations.

source_name: patient 17


title: NS09-748T-Xeno

description: gene expression profile

source_name: patient 22


title: NS08-568T-Xeno

description: gene expression profile

source_name: patient 18

value: R-GBM (IV)


title: NS08-559T-Xeno

description: gene expression profile

source_name: patient 13


title: NS07-448T-Xeno

description: gene expression profile

source_name: patient 14


title: NS10-783T-Xeno

description: gene expression profile

source_name: patient 24


title: NS09-690T-Xeno

description: gene expression profile

source_name: patient 21


title: NS08-578T-Xeno

description: gene expression profile

source_name: patient 19


title: NS07-437T-Xeno

description: gene expression profile


title: NS07-464T-Xeno

description: gene expression profile

source_name: patient 15


title: GBM11-082T-Xeno

description: gene expression profile

source_name: patient 10


title: GBM11-074T-Xeno

description: gene expression profile

source_name: patient 9


title: GBM11-096T-Xeno

description: gene expression profile

source_name: patient 11


title: GBM10-047T-Xeno

description: gene expression profile

source_name: patient 5


title: GBM10-050T-Xeno

description: gene expression profile

source_name: patient 6


title: NS08-541T-Xeno

description: gene expression profile

source_name: patient 16


title: GBM10-058T-Xeno

description: gene expression profile

source_name: patient 7


title: GBM11-099T-Xeno

description: gene expression profile

source_name: patient 12


title: GBM11-060T-Xeno

description: gene expression profile

source_name: patient 8


title: GBM10-025T-Xeno

description: gene expression profile

source_name: patient 1


title: GBM10-046T-Xeno

description: gene expression profile

source_name: patient 4


title: GBM10-039T-Xeno

description: gene expression profile

source_name: patient 2


title: GBM10-041T-Xeno

description: gene expression profile

source_name: patient 3


title: NS09-771T

description: gene expression profile

source_name: patient 69


title: NS10-783T

description: gene expression profile

source_name: patient 71


title: NS09-727T

description: gene expression profile

source_name: patient 67


title: NS09-700T

description: gene expression profile


title: NS09-774T

description: gene expression profile

source_name: patient 70


title: NS09-642T

description: gene expression profile

source_name: patient 57


title: NS09-676T

description: gene expression profile

source_name: patient 66


title: NS09-652T

description: gene expression profile

source_name: patient 65


title: NS09-732T

description: gene expression profile

source_name: patient 60


title: NS09-751T

description: gene expression profile

source_name: patient 68


title: NS08-615T

description: gene expression profile

source_name: patient 64


title: NS08-594T

description: gene expression profile

source_name: patient 58


title: NS08-499T

description: gene expression profile

source_name: patient 54


title: NS08-572T

description: gene expression profile

source_name: patient 63


title: NS07-773T

description: gene expression profile

source_name: patient 62


title: NS07-600T

description: gene expression profile

source_name: patient 34


title: NS08-538T

description: gene expression profile


title: NS09-750T

description: gene expression profile

source_name: patient 35


title: NS07-775T

description: gene expression profile

source_name: patient 9


title: NS07-470T

description: gene expression profile

source_name: patient 56


title: HaCaT_negative argon control_A60s

city: Greifswald

first: Anke

last: Schmidt

state: MV

address: Felix-Hausdorff-Str. 2

department: Plasma Life Science

country: Germany

institute: INP Greifswald

description: HaCaT treated negative control

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

scan_protocol: Scanning was performed by NimbleGen Systems Inc. MS 200, Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction was performed as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).

source_name: Argon gas-treated HaCaT

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

growth_protocol: The keratinocyte cell line (HaCaT), a human adult (low calcium, high temperature) epithelial keratinocyte cell line, was seeded at a density of one million cells in 6 cm dishes in RPMI (Roswell Park Memorial Institute 1640 cell culture media) supplemented with 8 % fetal calf serum (Sigma), 0.1 mg/mL penicillin/streptomycin and 2 mM L-glutamine (Lonza, Basel, Switzerland) and were left to attach for 24 h prior to plasma treatment.

extract_protocol: Total RNAs from each group (n>6) were purified using Total RNA Mini Kit (Bio&Sell, Germany) according to instructions including DNaseI treatment (Qiagen, Germany). RNA integrity was confirmed using the Bioanalyzer2010 (Agilent, Germany). cDNA was synthesized by SuperScript double-stranded cDNA Synthesis Kit (Invitrogen, Germany) from 10 µg of total RNA using oligodT primer (200 ng/mL). Double strand cDNAs were end-labeled with fluorescent Cy3-dye using a One-Color DNA Labeling Kit (Roche NimbleGen, Germany).

treatment_protocol: A non-thermal atmospheric pressure plasma jet kinpen (neoplas GmbH, Greifswald, Germany) ionized a flow of argon gas. A voltage of 2-6 kVpp was applied with a frequency of around 1 MHz. Gas flow was set to 3 sLm (standard liters per minute) which was controlled by a mass flow controller (MKS Instruments, Germany). The treatment time was to 20 s, 60 s, and 180 s corresponding to the following treatment time equivalents: 100, 300, and 900 ms*µL/cell, respectively after plasma treatment of 5 ml of RPMI medium were plasma-treated and immediately transferred to 1×106 cells (indirect treatment). Two hour after exposure to treated medium, cells were collected, centrifuged, and washed. Alternatively, cells were incubated with fresh media for another 1 h, 4 h, or 22 h. Cells treated with 100 µM H2O2 served as positive controls for oxidative stress. To exclude effects of the carrier gas, cells incubated with argon gas treated medium were used as negative controls. Subsequently, all samples were analyzed and compared in respect to their gene activity.

value: negative control


title: NS07-723T

description: gene expression profile

source_name: patient 37


title: HaCaT_negative argon control_A180s

description: HaCaT treated negative control


title: NS07-745T

description: gene expression profile

source_name: patient 61


title: HaCaT_positive H2O2 control_H100µM_6h

description: HaCaT treated positive control

source_name: H2O2-treated HaCaT

value: positive control


title: NS07-458T

description: gene expression profile


title: HaCaT_negative argon control_A20s

description: HaCaT treated negative control


title: NS07-465T

description: gene expression profile

source_name: patient 59


title: Control

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute for Molecular Bioscience, Uni of Qld

description: DNA was obtained from WTSI

hyb_protocol: Manufacturer protocol for SNP arrays (Illumina)

scan_protocol: Iscan Illumina

data_processing: GenomeStudio V2011.1 Genotype Module 1.9.4

source_name: cell line

label_protocol: Manufacturer protocol

extract_protocol: DNA was obtained from WTSI, according to the protocols in this publication: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145108/

value: Control

tag: cell line


title: NS07-567T

description: gene expression profile

source_name: patient 60


title: Melanoma

description: DNA was obtained from WTSI

value: Melanoma


title: HaCaT_plasma treated_P180s_6h, 2

description: HaCaT treated sample

source_name: plasma-treated HaCaT

value: non-thermal plasma treated sample


title: HaCaT_plasma treated_P180s_24h, 1

description: HaCaT treated sample


title: HaCaT_positive H2O2 control_H100µM_24h

description: HaCaT treated positive control


title: NS07-396T

description: gene expression profile

source_name: patient 55


title: NS09-775T-Xeno

description: gene expression profile

source_name: patient 23


title: HaCaT_plasma treated_P180s_6h, 3

description: HaCaT treated sample


title: HaCaT_plasma treated_P180s_24h, 3

description: HaCaT treated sample


title: NS07-412T

description: gene expression profile


title: HaCaT_plasma treated_P180s_24h, 2

description: HaCaT treated sample


title: HaCaT_positive H2O2 control_H100µM_3h

description: HaCaT treated positive control


title: HaCaT_plasma treated_P180s_6h, 1

description: HaCaT treated sample


title: NS07-424T

description: gene expression profile


title: HaCaT_plasma treated_P180s_3h, 3

description: HaCaT treated sample


title: NS07-428T

description: gene expression profile

source_name: patient 57


title: NS07-394T

description: gene expression profile

source_name: patient 54


title: NS07-421T

description: gene expression profile

source_name: patient 4


title: NS07-371T

description: gene expression profile

source_name: patient 53


title: HaCaT_plasma treated_P180s_3h, 2

description: HaCaT treated sample


title: NS07-372T-EC

description: gene expression profile

source_name: patient 30


title: HaCaT_plasma treated_P180s_3h, 1

description: HaCaT treated sample


title: HaCaT_plasma treated_P60s_24h, 2

description: HaCaT treated sample


title: HaCaT_plasma treated_P60s_24h, 3

description: HaCaT treated sample


title: HaCaT_plasma treated_P60s_24h, 1

description: HaCaT treated sample


title: NS06-314T

description: gene expression profile

source_name: patient 18


title: HaCaT_plasma treated_P60s_6h, 3

description: HaCaT treated sample


title: NS04-047T

description: gene expression profile

source_name: patient 51


title: IRCR_025HuGene-1_0-st-v1

description: gene expression profile

source_name: patient 41


title: HaCaT_plasma treated_P60s_6h, 1

description: HaCaT treated sample


title: HaCaT_plasma treated_P60s_6h, 2

description: HaCaT treated sample


title: NS06-265T

description: gene expression profile

source_name: patient 52


title: HaCaT_plasma treated_P60s_3h, 3

description: HaCaT treated sample


title: HaCaT_plasma treated_P60s_3h, 2

description: HaCaT treated sample


title: IRCR-GBM11-096T

description: gene expression profile

source_name: patient 50


title: HaCaT_plasma treated_P20s_24h, 1

description: HaCaT treated sample


title: IRCR-GBM10-027T

description: gene expression profile

source_name: patient 43


title: HaCaT_plasma treated_P20s_6h, 3

description: HaCaT treated sample


title: IRCR-GBM10-022T

description: gene expression profile

source_name: patient 42


title: IRCR-GBM10-058T

description: gene expression profile

source_name: patient 46


title: HaCaT_plasma treated_P60s_3h, 1

description: HaCaT treated sample


title: HaCaT_plasma treated_P20s_6h, 1

description: HaCaT treated sample


title: IRCR-GBM10-047T

description: gene expression profile

source_name: patient 45


title: HaCaT_plasma treated_P20s_24h, 2

description: HaCaT treated sample

source_name: plasma-treated HaCaT


title: IRCR-GBM11-074T

description: gene expression profile

source_name: patient 48


title: IRCR-GBM11-082T

description: gene expression profile

source_name: patient 49


title: HaCaT_plasma treated_P20s_3h, 2

description: HaCaT treated sample


title: IRCR-GBM10-016T

description: gene expression profile


title: IRCR-GBM10-041T

description: gene expression profile

source_name: patient 44


title: HaCaT_plasma treated_P20s_3h, 3

description: HaCaT treated sample


title: IRCR-GBM11-060T

description: gene expression profile

source_name: patient 47


title: HaCaT_plasma treated_P20s_6h, 2

description: HaCaT treated sample


title: GBM11-099T

description: gene expression profile


title: GBM10-050T

description: gene expression profile


title: GBM11-081T

description: gene expression profile


title: GBM10-046T

description: gene expression profile


title: CRA2/FOR2 (CGH)

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
Sample name: 63133702
Processed data file: Regions_of_Loss&Gain_Finch_CRA.csv
Platyspiza crassirostris-CRA (experimental) sample 2 is compared to Geospiza fortis-FOR (control) sample 2

hyb_protocol: For the copy number variation analysis a CGH custom design by Roche Nimblegen was used that consisted of a whole genome tiling array of Zebra Finch (Taeniopygia guttata) with 720,000 probes per array. The probe size ranged from 50-75mer in length with median probe spacing of 1395bp. Two different comparative (CNV vs CNV) hybridization experiments were performed (2 sub-arrays) for each species in query (FUL, SCA, PAR, CRA) versus control FOR, with each sub-array including hybridizations from DNA pools from these different species.  Two DNA pools were built for each species.

scan_protocol: Scanning and image acquisition was performed in-house by Nimblegen Inc.

data_processing:
For the CNV experiment raw data from the Cy3 and Cy5 channels were imported into R (R Development Core Team (2010), R: A language for statistical computing, R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org), checked for quality and converted to MA values (M=Cy5-Cy3; A=(Cy5+Cy3)/2).Within each array, probes were separated into groups by GC content and each group was separately normalized, between Cy3 and Cy5 using the loess normalization procedure. This allowed for GC groups to receive a normalization curve specific to that group. After each array was normalized within array, the arrays were then normalized across arrays using the A quantile normalization procedure. (Manikkam et al. 2012). Following normalization, the average value of each probe was calculated and three different copy number variation algorithms were used on each of these probes including circular binary segmentation from the DNA copy (Olshen et al. 2004), CGHseg (Picard et al. 2005) and cghFlasso (Tibshirani and Wang 2008).  These three algorithms were used with the default perimeters.  The average values from the output of these algorithms were obtained. A threshold of 0.04 as a cut-off was used on the summary (average of the log-ratio from the three algorithms) to specify gains and losses. Consecutive probes (≥3) of gains and losses were used to identify separate CNV regions. A cut-off of 3-probe minimum was used and those regions were considered a valid CNV.  The statistically significant copy number variation regions (CNV) were identified and P-values associated with each region presented. A cut-off of p < 10-5 was used to select the final regions of gains and losses. The July 2008 assembly of the Zebra Finch genome (taeGut1, WUSTL v3.2.4) produced by the Genome Sequencing Center at the Washington University in St. Louis (WUSTL) School of Medicine was retrieved (WUSTL 2008). A seed file was constructed and a BSgenome package was forged for using the Finch DNA sequence in the R code (Herve Pages BSgenome: Infrastructure for Biostrings-based genome data packages. R package version 1.24.0). This sequence was used to design the custom tiling arrays and to perform the bioinformatics. The chromosomal location of CNV and DMR clusters used an R-code developed to find chromosomal locations of clusters (M. K. Skinner et al. 2012).  A 2 Mb sliding window with 50,000 base intervals was used to find the associated CNV and DMR in each window.  A Z-test statistical analysis with p<0.05 was used on these windows to find the ones with over-represented CNV and DMR were merged together to form clusters.  A typical cluster region averaged approximately 3 megabases in size. The DMR and CNV association with specific zebra finch genes and genome locations used the Gene NCBI database for zebra finch gene locations and correlated the epimutations associated (overlapped) with the genes. The three adjacent probes constituted approximately a 200bp homology search. The KEGG pathway associations were identified by using the KEGG website 'Search Pathway' tool (M. K. Skinner et al. 2012). Statistically significant over-representation uses a Fisher’s exact analysis.  All DMR and CNV genomic data obtained in the current study have been deposited in the NCBI public GEO database. Spearman Rank correlation coefficients were used to test for a relationship between phylogenetic distance and epigenetic and genetic changes (Whitlock and Schluter 2009).
R-code data processing of raw data as described was used as the basis for conlusions in this study. Value definitions for processed data files (Regions_of_Loss&Gain_Finch_species): #Chromosome = Chromosome number, #cSTART = Cluster start site, #cSTOP = Cluster stop site, #RegionChanged = this is in Megabase, so the region (cSTOP-cSTART) divided by 1,000,000, when it is zero, it means single probe, #minP = p-value of that region showing how statistically significant that region is, P-value must be p<1.0E-5 or less for inclusion, #AverageLogRatio = average of logratio -since it has multiple arrays , #AverageSummary = average output of the three algorithm used to use for gain/loss threshold cut-off, #Gain.Loss = which regions were gain and which were losses, and #FORvs = compared finch species to reference species FOR. Other processed data files are included (arrayID#_segMNT.txt) but they were not used in our analysis.

organism: Platyspiza crassirostris

source_name: DNA from Platyspiza crassirostris (CRA) erythrocytes

label_protocol: For one sub-array of each species DNA samples from the experimental groups were labeled with Cy5 and DNA samples from the control lineage were labeled with Cy3. For the other sub-array of each species a dye swap was performed so that DNA samples from the experimental groups were labeled with Cy3 and DNA samples from the control lineage were labeled with Cy5.

growth_protocol: Birds were captured from January-April 2009 at El Garrapatero, a lowland arid site on Santa Cruz Island, Galapagos Archipelago, Ecuador, with mist nests and banded with numbered Monel bands to track recaptures.  Birds were identified, aged and sexed using size and plumage characteristics.

extract_protocol: A small blood sample (90 μl) from each bird was collected in a microcapillary tube via brachial venipuncture.  Samples were stored on wet ice in the field, then erythrocytes purified by centrifugation and cells stored in a -20˚C freezer at a field station.  Following the field season, samples were placed in a -80˚C freezer for longer term storage. Erythrocyte DNA was isolated with DNAeasy Blood and Tissue Kit (Qiagen, Valencia, CA) and then stored at -80°C prior to analysis.  DNA was sonicated as follows: DNA suspension was centrifuged at 500 × g for 5 min. The DNA was then resuspended in 5 ml NIM free of EDTA, PMSF, and leupeptin and centrifuged again. A small amount of DNA suspension (1 μl) was finally suspended in 5 μl of EDTA- and protease inhibitor-free NIM medium containing 12% polyvinyl pyrrolidone (PVP; Mr 360 000) (without protease inhibitors) (Tateno et al. 2000) and then purified using a series of washes and centrifugations (Ward et al. 1999) from variable number of animals per species analyzed. The same concentrations of DNA from individual blood samples were then used to produce pools of DNA material. Two DNA pools were produced in total per species, each one containing the same amount of DNA from different animals.  The number of individuals used per pool is shown in the manuscript's Supplemental Table S6. These DNA pools were then used for CGH arrays.

treatment_protocol: Experimental

tag: species (symbol)

value: Platyspiza crassirostris (CRA)

value: blood

value: erythrocytes

organism: Geospiza fortis

source_name: DNA from Geospiza fortis (FOR) erythrocytes

treatment_protocol: Control

value: Geospiza fortis (FOR)


title: PAR1/FOR1 (CGH)

description:
Sample name: 63133502
Processed data file: Regions_of_Loss&Gain_Finch_PAR.csv
Camarhynchus parvulus-PAR (experimental) sample 1 is compared to Geospiza fortis-FOR (control) sample 1

organism: Camarhynchus parvulus

source_name: DNA from Camarhynchus parvulus (PAR) erythrocytes

value: Camarhynchus parvulus (PAR)


title: HaCaT_untreated_controlK5

description: HaCaT untreated control

source_name: HaCaT control

value: untreated control


title: GBM10-031T

description: gene expression profile


title: FUL2/FOR2 (CGH)

description:
Sample name: 63132802
Processed data file: Regions_of_Loss&Gain_Finch_FUL.csv
G. fuliginosa-FUL (experimental) sample 2 is compared to Geospiza fortis-FOR (control) sample 2

organism: Geospiza fuliginosa

source_name: DNA from G. fuliginosa (FUL) erythrocytes

value: G. fuliginosa (FUL)


title: SCA1/FOR1 (CGH)

description:
Sample name: 63133602
Processed data file: Regions_of_Loss&Gain_Finch_SCA.csv
G. scandens-SCA (experimental) sample 1 is compared to Geospiza fortis-FOR (control) sample 1

organism: Geospiza scandens

source_name: DNA from G. scandens (SCA)  erythrocytes

value: G. scandens (SCA)


title: FUL1/FOR1 (CGH)

description:
Sample name: 63133102
Processed data file: Regions_of_Loss&Gain_Finch_FUL.csv
G. fuliginosa-FUL (experimental) sample 1 is compared to Geospiza fortis-FOR (control) sample 1


title: SCA2/FOR2 (CGH)

description:
Sample name: 63132602
Processed data file: Regions_of_Loss&Gain_Finch_SCA.csv
G. scandens-SCA (experimental) sample 2 is compared to Geospiza fortis-FOR (control) sample 2


title: CRA1/FOR1 (CGH)

description:
Sample name: 63132902
Processed data file: Regions_of_Loss&Gain_Finch_CRA.csv
Platyspiza crassirostris-CRA (experimental) sample 1 is compared to Geospiza fortis-FOR (control) sample 1


title: GBM10-039T

description: gene expression profile


title: HaCaT_untreated_controlK4

description: HaCaT untreated control


title: PAR2/FOR2 (CGH)

description:
Sample name: 63132702
Processed data file: Regions_of_Loss&Gain_Finch_PAR.csv
Camarhynchus parvulus-PAR (experimental) sample 2 is compared to Geospiza fortis-FOR (control) sample 2


title: HaCaT_plasma treated_P20s_24h, 3

description: HaCaT treated sample


title: GBM10-011T

description: gene expression profile


title: HaCaT_untreated_controlK2

description: HaCaT untreated control


title: GBM10-010T

description: gene expression profile


title: 827_1

description: gene expression profile


title: 748_tissue

description: gene expression profile

source_name: patient 40


title: 780HuGene-1_0-st-v1

description: gene expression profile

source_name: patient 41


title: HaCaT_untreated_controlK1

description: HaCaT untreated control


title: HaCaT_plasma treated_P20s_3h, 1

description: HaCaT treated sample


title: 690_tissue

description: gene expression profile

source_name: patient 38


title: 672_tissue

description: gene expression profile

source_name: patient 37


title: GBM10-023T

description: gene expression profile


title: 680_tissue

description: gene expression profile

source_name: patient 24


title: 696_tissue

description: gene expression profile

source_name: patient 39


title: 660_tissue

description: gene expression profile

source_name: patient 28


title: 663_tissue

description: gene expression profile

source_name: patient 26


title: HaCaT_untreated_controlK3

description: HaCaT untreated control


title: 740_tissue

description: gene expression profile

source_name: patient 36


title: 671_tissue

description: gene expression profile


title: 631_tissue

description: gene expression profile

source_name: patient 34


title: 602_tissue

description: gene expression profile

source_name: patient 29


title: 585_tissue

description: gene expression profile


title: 626_tissue

description: gene expression profile

source_name: patient 32


title: 609_tissue

description: gene expression profile

source_name: patient 31


title: 633_tissue

description: gene expression profile

source_name: patient 35


title: 647_tissue

description: gene expression profile

source_name: patient 27


title: 608_tissue

description: gene expression profile

source_name: patient 30


title: 578_cell

description: gene expression profile

source_name: patient 25


title: SP1KO hemogenic endothelium II (HE2) replicate2

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

hyb_protocol: Hybridization samples were prepared for a 8-pack microarray using 600 ng cRNA each according to the hybridization protocol from Agilent: One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling), loaded onto the 8-pack array slide and hybridized at 65 °C overnight

scan_protocol: After washing the microarray was scanned on an Agilent C Scanner using the Profile AgilentG3_GX_1Color for 8x60K microarrays (Dye channel: Green; Scan region: Scan Area (61 x 21.6 mm); Scan resolution (μm): 3; Tiff: 20 bit)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) (protocol GE1_107_Sep09, Grid: 028005_D_F_20100614 and platform Agilent SurePrint G3 Mouse GE 8x60K). The raw data output by Feature Extraction Software was analysed using the LIMMA R package with quantile normalization and background subtraction.

source_name: from differentiation of ES cells

label_protocol: 25ng of each source sample RNA was labelled with Cy3 dye as per the protocol detailed in the Low Input Quick Amp Labelling Kit (Agilent Technologies – 5190-2305). A Specific Activity of greater than 6.0 was confirmed by measurement of 260 nm and 550 nm wavelengths with a NanoDrop ND-1000 Spectrophotometer.

growth_protocol: ES cells were trypsinised and allowed to form embryoid bodies by plating in base methylcellulose (Stem Cell Technologies M3134) supplemented with 10% FCS, 100 units/ml Penicillin and 100 µg/ml Streptomycin, 1 mM glutamine, 0.15 mM MTG, 10 g/ml insulin (Sigma), 5% IL-3 conditioned media, 10 ng/ml recombinant mouse M-CSF (R&D Systems), 100 units/ml IL-1 (Peprotech) at a cell concentration previously determined to give similar numbers of EB. After at least 14 days EB were counted and assessed for the number of EB.

extract_protocol: RNA was extracted from cells using TRIzol® (Invitrogen) according to manufacturer’s instruction. First strand cDNA synthesis was carried out using Superscript II (Invitrogen) according to manufacturer’s instructions using 250-500 ng of RNA. Real Time PCR was carried out using ABI SYBR® green master mix with 5 µl of diluted cDNA and 0.25 µM primer per 15 µl reaction on an ABI 7900HT machine.

value: hemogenic endothelium II

tag: strain

tag: genotype

value: Sp1 -/- knock-out


title: SP1_KO_progenitor replicate2

tag: cell type

value: progenitor


title: SP1KO hemogenic endothelium I (HE1) replicate2

value: hemogenic endothelium I


title: 568_tissue

description: gene expression profile

source_name: patient 10

value: glioblastoma

value: R-GBM (IV)


title: SP1_KO_progenitor replicate1


title: 586_tissue

description: gene expression profile

value: GBM (IV)


title: 592_tissue

description: gene expression profile


title: 630_tissue

description: gene expression profile

source_name: patient 33


title: SP1KO hemogenic endothelium II (HE2) replicate1


title: 543_tissue

description: gene expression profile

source_name: patient 23


title: SP1KO hemogenic endothelium I (HE1) replicate1


title: 559_tissue

description: gene expression profile

source_name: patient 7


title: 577_tissue

description: gene expression profile

source_name: patient 24


title: SP1KO Flk+ replicate2

value: Flk+


title: E14 progenitor replicate2

value: Sp1 +/+ wild type


title: SP1KO Flk+ replicate1


title: E14 Flk+ replicate2


title: 541_tissue

description: gene expression profile

source_name: patient 22


title: S2-DRSC 2

city: Manchester

first: Suzanne

last: Hunt

address: Dover Street

department: Life Sciences

institute: University of Manchester

hyb_protocol: LC Sciences

scan_protocol: Axon GenePix 4000B Microarray Scanner, pixel = 10 µm

data_processing: Sample tables display background-subtracted raw signals without normalization. Normalized signals are available in the file "Normalized_Data.xls" on the series level. Data processing performed by LC Sciences.

organism: Drosophila melanogaster

source_name: Drosophila S2 cell line

label_protocol: LC Sciences

growth_protocol: D. melanogaster S2-DRSC cells were grown in 1 x Schneider’s media, supplemented with 10% FBS, 100 U/ml penicillin and 100 μg/ml streptomycin and incubated at 26°C.

extract_protocol: Total RNA was extracted from D. melanogaster S2-DRSC cells using the Ambion miRvana kit according to the manufacturer's instructions.


title: 531_tissue

description: gene expression profile

source_name: patient 20


title: E14 hemogenic endothelium II (HE2) replicate2


title: 532_tissue

description: gene expression profile

source_name: patient 21


title: S2-DRSC 1


title: 503_tissue

description: gene expression profile

source_name: patient 18


title: E14 Flk+ replicate1


title: E14 hemogenic endothelium I (HE1) replicate1


title: E14 progenitor replicate1


title: 498_tissue

description: gene expression profile

source_name: patient 17


title: E14 hemogenic endothelium I (HE1) replicate2


title: E14 hemogenic endothelium II (HE2) replicate1


title: 466_tissue

description: gene expression profile

source_name: patient 13


title: 464_tissue

description: gene expression profile

source_name: patient 12


title: 493_tissue

description: gene expression profile

source_name: patient 15


title: 492_tissue

description: gene expression profile

source_name: patient 14


title: 520_tissue

description: gene expression profile

source_name: patient 19


title: 463_tissue

description: gene expression profile

source_name: patient 11


title: 496_tissue

description: gene expression profile

source_name: patient 16


title: 460_tissue

description: gene expression profile

source_name: patient 10


title: 453_tissue

description: gene expression profile

source_name: patient 9


title: 448_cell

description: gene expression profile

source_name: patient 8


title: 437_tissue

description: gene expression profile

source_name: patient 7


title: 435_tissue

description: gene expression profile

source_name: patient 5


title: 52 somites, sample 1

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

description: 52 somite 1

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned GenePix 4100A at a resolution of 5 microns

data_processing: GenePix Pro 6.0 was used for spot to grid alignment, feature extraction and quantification. After removal of flagged spots lowess normalization was performed

organism: Gadus morhua

source_name: Embryos 52 somite pairs

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

growth_protocol: Atlantic cod eggs and embryos were obtained from farmed fish at the National Cod Breeding Centre (Kraknes, Tromsø, Norway). Eggs were hand stripped, fertilized in vitro and transferred to seawater rearing tanks at an average temperature of 4.5°C and 100% oxygen saturation.

extract_protocol: RNA was isolated using the iPrep™ TRIzol® Plus kit (Invitrogen), and purified with RNeasy mini kit (QIAGEN)

treatment_protocol: No treatment

value: Embryos 52 somite pairs

source_name: common reference

tag: age

value: adult

value: Mixture of organs


title: 436_tissue

description: gene expression profile

source_name: patient 6


title: 52 somites, sample 2

description: 52 somite 2


title: Mid blastula, sample 3

description: MBT 3

source_name: Mid blastula

value: Mid blastula


title: 12 somites, sample 1

description: 12 somite 1

source_name: Embryos 12 somite pairs

value: Embryos 12 somite pairs


title: Oocytes 2 hours post fertilization, sample 1

description: 2 hpf 1

source_name: Ooocytes 2 hpf

value: Ooocytes 2 hpf


title: 380_tissue

description: gene expression profile

source_name: patient 2


title: 12 somites, sample 2

description: 12 somite 2


title: 386_tissue

description: gene expression profile

source_name: patient 4


title: 357_tissue

description: gene expression profile

source_name: patient 1


title: Mid blastula, sample 2

description: MBT 2


title: Oocytes 2 hours post fertilization, sample 2

description: 2 hpf 2


title: Mid blastula, sample 1

description: MBT 1


title: Oocytes 2 hours post fertilization, sample 3

description: 2 hpf 3


title: miR-142 KO FL-MKs, rep1

status: Public on Jun 11 2014

city: Rehovot

first: Elik

last: Chapnik

address: Herzel st.

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
EH82a
miR-142 knockout fetal liver-derived MKs, biological replicate 1
Gene expression data from miR-142 knockout fetal liver-derived MKs, biological replicate 1

hyb_protocol: RNA was hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST arrays

scan_protocol: According to Affymetrix manual

data_processing: Affymetrix Expression Console was used, followed by normalization of all arrays together using GC-RMA.

label_protocol: According to Affymetrix manual

growth_protocol: Fetal liver cells were maintained in Dulbecco modified Eagle medium (DMEM; Invitrogen) supplemented with 10% fetal bovine serum (FBS; Invitrogen), 100 U/ml penicillin, 100µg/ml streptomycin, and 50ng/ml recombinant human thrombopoietin (TPO; Peprotech).

tag: developmental stage

value: fetus

value: liver

value: MK

tag: genotype/variation

value: miR-142 knockout


title: 381_tissue

description: gene expression profile

source_name: patient 3


title: WT FL-MKs, rep2

description:
EH81a
wild-type fetal liver-derived MKs, biological replicate 2
Gene expression data from wild-type fetal liver-derived MKs, biological replicate 2

source_name: wild-type fetal liver-derived MKs

value: wild-type


title: Unfertilized oocytes, sample 2

source_name: Unfertilized oocytes

value: Unfertilized oocytes


title: Unfertilized oocytes, sample 1


title: Unfertilized oocytes, sample 3


title: WT FL-MKs, rep1

description:
EH80a
wild-type fetal liver-derived MKs, biological replicate 1
Gene expression data from wild-type fetal liver-derived MKs, biological replicate 1


title: tr_24h_465

city: Berlin

first: Maria

last: Reichenbach

address: Thielallee 63

department: Institute for Chemistry and Biochemistry

institute: Freie Universität Berlin

description:
Gene expression after 24h cyclic mechanical stretching
Reu_34

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies) (Design ID 028004). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized 17 h at 65°C to Agilent whole genome oligo microarrays 8X60K using Agilent's recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression wash buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression wash buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent microarrays were detected using Agilent's Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA)..

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files. The preprocessing proper started with the conversion of the data after using Agilent Feature Extraction software in a format suitable for all subsequent analysis steps, which were mainly performed with the R statistical software and its Bioconductor packages. For the preprocessing the agi4x44kpreprocess package was used. To  this  end  an annotation package for the Agilent Whole Genome 8x60K chip has (previously) been created. After reading the data files into R, all data were background-corrected. Data were then normalized between arrays using quantile-normalization and transformed to log2-scale, which enabled comparison of samples loaded on different arrays. After normalization, a set of quality control steps were performed to filter low-quality probes. Filtering of probes was based on quality flags set by the Agilent Feature Extraction Software. Most of the probes (~42 %) were filtered because of not being sufficiently above background. Finally, the processed data were stored in formats that allowed further downstream analyses and easy access.

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 24h, subject 7

label_protocol: For the linear T7-based amplification step, 100ng of each total RNA sample was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol. Yields of cRNA and the dye-incorporation rate were measured with ND-1000 Spectrophotometer (NanoDrop Technologies)

growth_protocol: Primary human dermal fibroblasts were isolated from skin biopsies obtained from plastic surgery by collagenase digestion and stored at -170°C in DMSO until usage. All donors provided written, informed consent. For experiments cells were cultured only until the third passage in Dulbecco’s modified Eagle’s Medium (DMEM, 4.5 g/l glucose) containing 10% fetal calf serum, 2 mM L-alanyl-L-glutamine and 0.1 mg/ml penicillin/streptomycin at 37°C in an atmosphere of 5% CO2 and 90% humidity.

extract_protocol: To separate the inhomogeneous stretching areas of the BioFlex culture plates the silicon membranes were punched with a 2 cm diameter punch. Isolation of RNA was done with Rneasy Mini kit according to manufacturer product information from the outer cicular region of the well. DNA and RNA were precipitated with 70 % ethanol and bound to a column. DNA was digested using DNAse I. RNA was eluted with 30 µl RNAse free water and subjected to Experion automated electrophoresis using the Experion RNA StdSens Analysis Kit (Bio-Rad, Hercules, USA)  for quality control.

treatment_protocol: Mechanical stretching was performed on flexible silicon membranes using FX-4000T™ Tension Plus™ System (Flexercell International Corporation, Hillsborough, USA). Cells were seeded on Bioflex culture plates and after 24 h subjected to stretching experiments or left untreated as control. Cyclic stretch was applied for 5 h and 24 h in the FX-4000T ™ Tension Plus™ System with 16% Elongation, 0.5 Hz in a half sinus regimen. Cell alignment was observed at the outer circular region of the well. Control cells were left static for 5 h and 24 h, as well.

tag: individual

value: subject 7

value: primary dermal fibroblasts

value: cyclic mechanical stretching


title: miR-142 KO FL-MKs, rep2

description:
EH83a
miR-142 knockout fetal liver-derived MKs, biological replicate 2
Gene expression data from miR-142 knockout fetal liver-derived MKs, biological replicate 2


title: tr_24h_445

description:
Gene expression after 24h cyclic mechanical stretching
Reu_40

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 24h, subject 10

value: subject 10

tag: treatment


title: tr_5h_387

description:
Gene expression after 5h cyclic mechanical stretching
Reu_37

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 5h, subject 9

value: subject 9

tag: time


title: tr_5h_445

description:
Gene expression after 5h cyclic mechanical stretching
Reu_39

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 5h, subject 10


title: tr_24h_416

description:
Gene expression after 24h cyclic mechanical stretching
Reu_32

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 24 h, subject 6

value: subject 6


title: tr_24h_446

description:
Gene expression after 24h cyclic mechanical stretching
Reu_36

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 24h, subject 8

value: subject 8


title: tr_5h_464

description:
Gene expression after 5h cyclic mechanical stretching
Reu_25

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 5h, subject 3

value: subject 3


title: tr_5h_465

description:
Gene expression after 5h cyclic mechanical stretching
Reu_33

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 5h, subject 7


title: tr_24h_425

description:
Gene expression after 24h cyclic mechanical stretching
Reu_28

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 24h, subject 4

value: subject 4


title: tr_5h_420

description:
Gene expression after 5h cyclic mechanical stretching
Reu_23

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 5h, subject 2

value: subject 2


title: tr_5h_446

description:
Gene expression after 5h cyclic mechanical stretching
Reu_35

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 5h, subject 8


title: tr_5h_432

description:
Gene expression after 5h cyclic mechanical stretching
Reu_29

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 5h, subject 5

value: subject 5


title: tr_24h_420

description:
Gene expression after 24h cyclic mechanical stretching
Reu_24

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 24h, subject 2


title: tr_5h_416

description:
Gene expression after 5h cyclic mechanical stretching
Reu_31

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 5h, subject 6


title: tr_24h_432

description:
Gene expression after 24h cyclic mechanical stretching
Reu_30

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 24h, subject 5


title: tr_24h_392

description:
Gene expression after 24h cyclic mechanical stretching
Reu_22

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 24h, subject 1

value: subject 1


title: co_5h_445

description:
Gene expression after 5h cell culture
Reu_19

source_name: untreated primary human dermal fibroblasts, 5h, subject 10

value: static


title: tr_5h_392

description:
Gene expression after 5h cyclic mechanical stretching
Reu_21

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 5h, subject 1


title: tr_5h_425

description:
Gene expression after 5h cyclic mechanical stretching
Reu_27

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 5h, subject 4


title: co_5h_387

description:
Gene expression after 5h cell culture
Reu_17

source_name: untreated primary human dermal fibroblasts, 5h, subject 9


title: co_24h_387

description:
Gene expression after 24h cell culture
Reu_18

source_name: untreated primary human dermal fibroblasts, 24h, subject 9


title: co_24h_446

description:
Gene expression after 24h cell culture
Reu_16

source_name: untreated primary human dermal fibroblasts, 24h, subject 8


title: tr_24h_464

description:
Gene expression after 24h cyclic mechanical stretching
Reu_26

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 24h, subject 3


title: co_24h_445

description:
Gene expression after 24h cell culture
Reu_20

source_name: untreated primary human dermal fibroblasts, 24h, subject 10


title: co_24h_432

description:
Gene expression after 24h cell culture
Reu_10

source_name: untreated primary human dermal fibroblasts, 24h, subject 5


title: co_5h_465

description:
Gene expression after 5h cell culture
Reu_13

source_name: untreated primary human dermal fibroblasts, 5h, subject 7


title: co_24h_464

description:
Gene expression after 24h cell culture
Reu_6

source_name: untreated primary human dermal fibroblasts, 24h, subject 3


title: co_5h_446

description:
Gene expression after 5h cell culture
Reu_15

source_name: untreated primary human dermal fibroblasts, 5h, subject 8


title: co_24h_420

description:
Gene expression after 24h cell culture
Reu_4

source_name: untreated primary human dermal fibroblasts, 24h, subject 2


title: Duroc x Iberian piglet 10

city: Madrid

first: Cristina

last: Ovilo

address: Ctra Coruña km 7.5

country: Spain

institute: INIA-CSIC

description: Gene expression data from l.dorsi muscle tissue of male DUROC x IBERIAN pig at 28 days of age

hyb_protocol: standard Affymetrix hybridization protocol

scan_protocol: standard Affymetrix scanning protocol using GCOS

data_processing: Expression data were generated with GeneChip Operating Software (GCOS, Affymetrix) and GCRMA normalization was carried out with BRB-Array Tools (v.3.6.0), by filtering out those probes with minimal variation across the set of arrays. Only genes displaying more than 20% of expression values over ± 1.5 times the median expression of all arrays were used for further analysis (5226 probes)

organism: Sus scrofa

source_name: Longissimus dorsi muscle

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

growth_protocol: Animals were mantained and feeded by their mothers until sacrifice, which was performed by the time of weaning (28 days of age)

extract_protocol: RiboPure RNA isolation kit

treatment_protocol: Muscle tissue samples  obtained at slaughter were mantained at -80ºC until processing for RNA extraction

value: Duroc x Iberian

value: Longissimus dorsi muscle

tag: gender

value: Male

value: 28 days of age


title: Duroc x Iberian piglet 14


title: Duroc x Iberian piglet 13


title: co_5h_416

description:
Gene expression after 5h cell culture
Reu_11

source_name: untreated primary human dermal fibroblasts, 5h, subject 6


title: co_5h_432

description:
Gene expression after 5h cell culture
Reu_9

source_name: untreated primary human dermal fibroblasts, 5h, subject 5


title: co_5h_464

description:
Gene expression after 5h cell culture
Reu_5

source_name: untreated primary human dermal fibroblasts, 5h, subject 3


title: co_24h_465

description:
Gene expression after 24h cell culture
Reu_14

source_name: untreated primary human dermal fibroblasts, 24h, subject 7

value: subject 7


title: co_5h_392

description:
Gene expression after 5h cell culture
Reu_1

source_name: untreated primary human dermal fibroblasts, 5h, subject 1

value: primary dermal fibroblasts


title: Duroc x Iberian piglet 9


title: Duroc x Iberian piglet 8


title: Duroc x Iberian piglet 11


title: Duroc x Iberian piglet 12


title: co_24h_416

description:
Gene expression after 24h cell culture
Reu_12

source_name: untreated primary human dermal fibroblasts, 24 h, subject 6


title: Duroc x Iberian piglet 6


title: Duroc x Iberian piglet 5


title: Duroc x Iberian piglet 4


title: co_5h_425

description:
Gene expression after 5h cell culture
Reu_7

source_name: untreated primary human dermal fibroblasts, 5h, subject 4


title: co_5h_420

description:
Gene expression after 5h cell culture
Reu_3

source_name: untreated primary human dermal fibroblasts, 5h, subject 2


title: Duroc x Iberian piglet 2


title: Duroc x Iberian piglet 1


title: co_24h_392

description:
Gene expression after 24h cell culture
Reu_2

source_name: untreated primary human dermal fibroblasts, 24h, subject 1


title: Duroc x Iberian piglet 3


title: Duroc x Iberian piglet 7


title: co_24h_425

description:
Gene expression after 24h cell culture
Reu_8

source_name: untreated primary human dermal fibroblasts, 24h, subject 4


title: Iberian piglet 7

description: Gene expression data from l.dorsi muscle tissue of male IBERIAN pig at 28 days of age

value: Iberian


title: Iberian piglet 8


title: Iberian piglet 9


title: Iberian piglet 6


title: Iberian piglet 5


title: Iberian piglet 4


title: Iberian piglet 12


title: Iberian piglet 10


title: Iberian piglet 11


title: Iberian piglet 13


title: Iberian piglet 14


title: Iberian piglet 2


title: Iberian piglet 3


title: Iberian piglet 1


title: 5556 NOTCH3 +/- (aorta)

city: Boston

first: Joseph

last: Arboleda-Velasquez

address: 20 Staniford st

department: Opthalmology

institute: Schepens Eye Research Institute

description: gene expression data from Notch3 heterozygous 10-12 week old males compared to 10-12 week old male Notch3 knockouts

hyb_protocol: Biotinylated cRNA samples (four Notch 3 +/− mice or Notch 3 −/− mice) were fragmented before hybridization (15 μg each) onto mouse 430 2.0 Affymetrix chips.

scan_protocol: The chips were washed, stained by using strepavidin-phycoerytrin, and scanned the next day

data_processing: For data normalization, all probe sets were scaled to a target intensity of 150. Microarray data analysis was performed by using Rosetta Resolver. All cells were from 10- to 12-week-old male mice.

source_name: 10-12 week old male mice heterozygous for Notch3

label_protocol: cRNA samples were biotinylated

extract_protocol: FOR BRAIN: FACS sorted brain-derived SMC/pericyte cells were sorted into RNA extraction buffer (RNAeasy, Qiagen) supplemented with 3% beta-mercaptoethanol and purifed according to the manufacturers instructions. Samples were treated with DNAse prior to analysis (Invitrogen). All samples were controlled for RNA quality by microcapillary electrophoresis (RNA 6000 Nano and RNA 6000 Pico Assays, Agilent Technologies. Only the samples showing RNA integrity as judged by the presence of sharp 18S and 28S ribosomal RNA peaks, and displaying no obvious signs or RNA degradation in the fluorograms were considered for subsequent microarray hybridization. FOR AORTA: RNA was extracted from aorta explants using Trizol and the PureLink purification reagents (Invitrogen) and later purified again with the RNAeasy kit (Qiagen) and treated with DNAse prior to analysis Invitrogen).All samples were controlled for NA quality by microcapillary electrphoresis (RNA 6000 Nano and RNA 6000 Pico Assays, Agilent Technologies. Only the samples showing RNA integrity as judged by the presnece of sharp 18S and 28S ribosomal RNA peaks, and displaying no obvious signs or RNA degradation in the fluorgrams were considered for subsequent microarray hybridization

value: 10-12 weeks

value: male

value: NOTCH3 +/-

value: aorta explants


title: 6166 NOTCH3 +/- (aorta)


title: 5558 NOTCH3 -/- (aorta)

source_name: 10-12 week old male mice knockout Notch3

value: NOTCH3 -/-


title: 5561 NOTCH3 +/- (aorta)


title: H NOTCH3 +/- (brain)

value: FACS sorted brain-derived SMC/pericyte cells


title: D NOTCH3 -/- (brain)


title: G NOTCH3 +/- (brain)


title: B NOTCH3 -/- (brain)


title: 6167 NOTCH3 -/- (aorta)


title: AhR KO 2d Imiquimod 3

city: London

first: Gitta

last: Stockinger

address: The Ridgeway

department: Division of Molecular Immunology

institute: National Institute for Medical Research

description: biological replicate 3

hyb_protocol: User guide Affymetrix GeneChip 3’ Express Kit (P/N 702646 Rev.8)

scan_protocol: User guide Affymetrix Expression Wash, Stain and Scan (P/N 702731 Rev. 3)

data_processing: The data were RMA normalized using R package affy (Bolstad et al., 2003) that is a part of the Bioconductor project http://www.bioconductor.org.

source_name: AhR KO 2d Imiquimod

growth_protocol: Skin samples were collected at day 0 or day 2 following initiation of imiquimod treatment.

extract_protocol: Total RNA from mouse skin was obtained using a Polytron PT 3000 tissue homogenizer (Kinematika) along with TRIzol (Life technologies), according to the manufacturers’ instructions.

treatment_protocol: Skin samples were snap-frozen immediately after collection.

value: AhR-/-

tag: tissue type

value: skin


title: 5559 NOTCH3 -/- (aorta)


title: A NOTCH3 -/- (brain)


title: E NOTCH3 +/- (brain)


title: tr_24h_387

description:
Gene expression after 24h cyclic mechanical stretching
Reu_38

source_name: cyclic mechanical stretched primary human dermal fibroblasts, 24h, subject 9

value: subject 9

value: cyclic mechanical stretching


title: C NOTCH3 -/- (brain)


title: AhR KO 2d Imiquimod 1

description: biological replicate 1

label_protocol: User guide Affymetrix GeneChip 3’ Express Kit (P/N 702646 Rev.8)


title: AhR HET 2d Imiquimod 2

description: biological replicate 2

source_name: AhR HET 2d Imiquimod

value: AhR+/-


title: AhR KO 2d Imiquimod 2

description: biological replicate 2


title: AhR HET 2d Imiquimod 1

description: biological replicate 1


title: AhR HET 2d Imiquimod 3

description: biological replicate 3


title: I NOTCH3 +/- (brain)


title: AhR KO untreated 3

description: biological replicate 3

source_name: AhR KO untreated


title: F NOTCH3 -/- (brain)


title: AhR HET untreated 2

description: biological replicate 2

source_name: AhR HET untreated


title: AhR HET untreated 3

description: biological replicate 3


title: AhR KO untreated 2

description: biological replicate 2


title: AhR HET untreated 1

description: biological replicate 1


title: 806-28-Uns-M

city: Oxford

first: Magali

last: Matsumiya

address: Roosevelt Drive

department: Jenner Institute

institute: University of Oxford

hyb_protocol: Illumina HT-12 v4 kit according to manufacturer's instructions

scan_protocol: Illumina iScan machine scanned to produce summary idat files. Idat files read by genome studio with no correction or background subtraction

data_processing: Data processing done in R using the following packages: limma (excluding probes with detection p value >0.05 in all samples) and normalising with neqc using the control probes.

source_name: PBMC

label_protocol: Ambion Illumina Totalprep  and Illumina chip kits according to manufacturer's instructions

extract_protocol: Qiagen RNeasy kit according to instructions including DNase I digest

treatment_protocol: PBMC extracted in CPT tubes and cryopreserved. PBMC thawed and rested overnight with benzonase then counted on a casy counter and 1-2 million cells stimulated with R10 media alone (uns) or containing Ag85A peptides (A85A) for 12 hours. PBMC pelleted and frozen in 350uL Qiagen RLT buffer containing beta-mercaptoethanol.

tag: simulation

value: Unstimulated

tag: vaccine

tag: volunteer


title: 386-0-Uns-M


title: 414-0-Uns-M


title: AhR KO untreated 1

description: biological replicate 1


title: 760-28-Uns-C

value: Candin placebo


title: 386-28-Uns-M


title: 492-0-Uns-C


title: 927-28-Uns-M


title: 756-0-A85A-C


title: 624-28-Uns-M


title: 457-28-A85A-M


title: 492-28-Uns-C


title: 927-0-Uns-M


title: 756-28-A85A-C


title: 939-28-A85A-C


title: 426-28-Uns-C


title: 467-0-Uns-C


title: 467-28-Uns-C


title: 984-28-A85A-M


title: 756-28-Uns-C


title: 760-0-Uns-C


title: 939-0-A85A-C


title: 806-0-Uns-M


title: 771-0-A85A-M


title: 771-28-Uns-M


title: 939-28-Uns-C


title: 426-0-Uns-C


title: 984-0-A85A-M


title: 756-0-Uns-C


title: 771-28-A85A-M


title: 624-0-Uns-M


title: 984-0-Uns-M


title: 623-0-Uns-C


title: 939-0-Uns-C


title: 457-28-Uns-M


title: 457-0-Uns-M


title: 621-28-Uns-M


title: 673-28-Uns-M


title: 347-0-Uns-C


title: 347-28-A85A-C


title: 771-0-Uns-M


title: 528-0-A85A-M


title: 994-28-A85A-M


title: 849-0-Uns-M


title: 994-0-Uns-M


title: 990-0-Uns-M


title: 636-28-Uns-C


title: 847-0-Uns-M


title: 621-0-Uns-M


title: 457-0-A85A-M


title: 471-28-Uns-C


title: 413-0-Uns-M


title: 615-28-Uns-C


title: 984-28-Uns-M


title: 990-28-A85A-M


title: 471-0-Uns-C


title: 636-0-Uns-C


title: 662-0-Uns-C


title: 615-0-Uns-C


title: 528-0-Uns-M


title: 465-28-Uns-M


title: 662-28-A85A-C


title: 990-28-Uns-M


title: 662-0-A85A-C


title: 465-0-Uns-M


title: 528-28-A85A-M


title: 994-0-A85A-M


title: 849-0-A85A-M


title: 347-28-Uns-C


title: 413-28-Uns-M


title: 396-0-Uns-M


title: 348-0-Uns-C


title: 994-28-Uns-M


title: 847-28-Uns-M


title: 396-28-Uns-M


title: 348-28-Uns-C


title: 990-0-A85A-M


title: 662-28-Uns-C


title: WBday1-168-C

source_name: whole blood, heelprick

extract_protocol: Qiagen RNeasy kit with the following modifications: 80% EtOH (rather than 70%) and an extra wash with buffer RW1 prior to DNase I digest

treatment_protocol: 50-300uL whole blood was collected using a BD Quickheel lancet from the heel 1 day post-vaccination. The whole blood was collected directly into Qiagen RLT buffer containing beta-mercaptoethanol and frozen immediately.


title: WBday1-140-M


title: 528-28-Uns-M


title: 673-0-Uns-M


title: WBday1-257-M


title: WBday1-322-M


title: WBday1-132-M


title: WBday1-123-C


title: WBday1-322-C


title: WBday1-253-C_J


title: WBday1-102-C_H


title: WBday1-60-M


title: WBday1-101-C


title: WBday1-86-M


title: WBday1-385-M


title: WBday1-116-M


title: WBday1-250-C


title: WBday1-355-C


title: WBday1-212-C


title: 623-28-Uns-C


title: WBday1-186-M


title: WBday1-245-C


title: WBday1-143-C


title: WBday1-136-C


title: WBday1-119-M_D


title: WBday1-101-M_I


title: WBday1-201-M


title: WBday1-140-C


title: WBday1-142-C_K


title: WBday1-262-M


title: WBday1-185-C


title: WBday1-125-M_K


title: WBday1-169-M


title: WBday1-243-C


title: WBday1-194-M


title: WBday1-272-M


title: WBday1-286-C


title: WBday1-658-M


title: WBday1-99-M


title: WBday1-183-C_K


title: WBday1-119-M_G


title: WBday1-218-C


title: WBday1-276-C


title: WBday1-110-M


title: WBday1-145-C


title: WBday1-266-M


title: WBday1-183-M


title: WBday1-164-C


title: WBday1-153-C


title: WBday1-392-M


title: WBday1-175-C


title: WBday1-204-C


title: WBday1-182-M


title: WBday1-118-C


title: WBday1-259-C


title: WBday1-123-M


title: WBday1-367-C


title: WBday1-192-C


title: WBday1-149-C


title: WBday1-291-M


title: WBday1-261-M


title: WBday1-127-C


title: WBday1-118-M


title: WBday1-165-C


title: WBday1-131-C


title: WBday1-195-C


title: WBday1-102-C_L


title: WBday1-151-M


title: WBday1-125-M_G


title: WBday1-142-C_B


title: WBday1-210-M


title: WBday1-183-C_L


title: WBday1-101-M_A


title: WBday1-398-M


title: WBday1-253-C_B


title: WBday1-92-C


title: WBday1-193-C


title: WBday1-231-M


title: WBday1-202-M


title: WBday1-169-C


title: WBday1-150-C


title: WBday1-231-C


title: WBday1-550-C


title: WBday1-185-M


title: Blood_0_576

city: Gyeonggi-do

first: Boyoung

last: Park

address: 323 Ilsan-ro, Ilsandong-gu, Goyang-si

institute: National Cancer Centerm Korea

description: Hybridized to Axiom®_Exome_319

hyb_protocol: Following hybridization, the bound target is washed under stringent conditions to remove non-specific background to minimize background noise caused by random ligation events. Each polymorphic nucleotide is queried via a multi-color ligation event carried out on the array surface.

scan_protocol: After ligation, the arrays are stained and imaged on the GeneTitan MC Instrument (Affymetrix, Santa Clara, CA, USA)

data_processing: Using rawdata(cel files) as input, data analysis was conducted by Affymetrix power tools(APT) in linux server. APT-probeset-gneotype program, one of the APT applications, was used to gain genotype call as well as CHP files, which was run by birdseed-v2 algorithm as analysis option.

label: Biotin

source_name: peripheral blood leukocytes_control

label_protocol: About 200ng of genomic DNA is amplified and randomly fragmented into 25 to 125 base pair (bp) fragments. gDNA initial amplification reacted in 40㎕ reaction volume, containing 20㎕ volume of genomic DNA at a concentration of 10ng/㎕, 20㎕ of Denaturation Master Mix. The reaction of initial amplification carried out as follows: 10min at Room Temperature. After the initial amplification, the incubated products were amplicated with 130㎕ of Axiom 2.0 Neutral Soln, 225㎕ Axiom 2.0 Amp Soln and 5㎕ Axiom 2.0 Amp Enzyme. The amplification reactions were carried out as follows: 23hour ± 1hour at 37℃. The amplification products were performed in optimized reaction to amplify fragments between 200-1,100 base pairs. A fragmentation step then reduced the amplified products to segments of approximately 25-50 bp, which were then end-labeled using biotinylated nucleotides.

growth_protocol: Peripheral blood drawn from venous was stored in an icebox after obtaining to keep cool and was centrifused within one hour. After discarding supernatant, the blood was isolated as serum, plasma, RBC, whole blood, and buffy coat and stored in cryotube.

extract_protocol: After the blood samples are thawed, standard citrate buffer is added, mixed, and the tubes are centrifuged and the top portion of the supernatant is discarded (twice). The pellet is resuspended in a solution of SDS detergent and proteinase K, and the mixture is incubated at 55deg C for one hour. The sample then is phenol extracted once with a phenol/chloroform/isoamyl alcohol solution, and after centrifugation the aqueous layer is removed to a fresh microcentrifuge tube. The DNA is ethanol precipitated, resuspended in buffer, and then ethanol precipitated a second time. Once the pellet is dried, buffer is added and the DNA is resuspended by incubation.

treatment_protocol: The isolated samples are stored in -80deg C deep freezer.

tag: group

value: control

value: female


title: Blood_0_570

description: Hybridized to Axiom®_Exome_319


title: Blood_0_564

description: Hybridized to Axiom®_Exome_319


title: Blood_0_560

description: Hybridized to Axiom®_Exome_319


title: Blood_0_568

description: Hybridized to Axiom®_Exome_319


title: Blood_0_565

description: Hybridized to Axiom®_Exome_319


title: Blood_0_575

description: Hybridized to Axiom®_Exome_319


title: Blood_0_574

description: Hybridized to Axiom®_Exome_319


title: Blood_0_567

description: Hybridized to Axiom®_Exome_319


title: Blood_0_572

description: Hybridized to Axiom®_Exome_319


title: Blood_0_561

description: Hybridized to Axiom®_Exome_319


title: Blood_0_563

description: Hybridized to Axiom®_Exome_319


title: Blood_0_571

description: Hybridized to Axiom®_Exome_319


title: Blood_0_556

description: Hybridized to Axiom®_Exome_319


title: Blood_0_562

description: Hybridized to Axiom®_Exome_319


title: Blood_0_555

description: Hybridized to Axiom®_Exome_319


title: Blood_0_552

description: Hybridized to Axiom®_Exome_319


title: Blood_0_553

description: Hybridized to Axiom®_Exome_319


title: Blood_0_551

description: Hybridized to Axiom®_Exome_319


title: Blood_0_569

description: Hybridized to Axiom®_Exome_319


title: Blood_0_573

description: Hybridized to Axiom®_Exome_319


title: Blood_0_550

description: Hybridized to Axiom®_Exome_319


title: Blood_0_566

description: Hybridized to Axiom®_Exome_319


title: Blood_0_554

description: Hybridized to Axiom®_Exome_319


title: Blood_0_548

description: Hybridized to Axiom®_Exome_319


title: Blood_0_557

description: Hybridized to Axiom®_Exome_319


title: Blood_0_559

description: Hybridized to Axiom®_Exome_319


title: Blood_0_558

description: Hybridized to Axiom®_Exome_319


title: Blood_0_549

description: Hybridized to Axiom®_Exome_319


title: Blood_0_547

description: Hybridized to Axiom®_Exome_319


title: Blood_0_545

description: Hybridized to Axiom®_Exome_319


title: Blood_0_544

description: Hybridized to Axiom®_Exome_319


title: Blood_0_543

description: Hybridized to Axiom®_Exome_319


title: Blood_0_542

description: Hybridized to Axiom®_Exome_319


title: WBday1-174-C


title: Blood_0_541

description: Hybridized to Axiom®_Exome_319


title: Blood_0_538

description: Hybridized to Axiom®_Exome_319


title: Blood_0_539

description: Hybridized to Axiom®_Exome_319


title: Blood_0_534

description: Hybridized to Axiom®_Exome_319


title: Blood_0_531

description: Hybridized to Axiom®_Exome_319


title: Blood_0_533

description: Hybridized to Axiom®_Exome_319


title: Blood_0_535

description: Hybridized to Axiom®_Exome_319


title: Blood_0_530

description: Hybridized to Axiom®_Exome_319


title: Blood_0_532

description: Hybridized to Axiom®_Exome_319


title: Blood_0_537

description: Hybridized to Axiom®_Exome_319


title: Blood_0_528

description: Hybridized to Axiom®_Exome_319


title: Blood_0_526

description: Hybridized to Axiom®_Exome_319


title: Blood_0_540

description: Hybridized to Axiom®_Exome_319


title: Blood_0_522

description: Hybridized to Axiom®_Exome_319


title: Blood_0_536

description: Hybridized to Axiom®_Exome_319


title: Blood_0_546

description: Hybridized to Axiom®_Exome_319


title: Blood_0_525

description: Hybridized to Axiom®_Exome_319


title: Blood_0_523

description: Hybridized to Axiom®_Exome_319


title: Blood_0_520

description: Hybridized to Axiom®_Exome_319


title: Blood_0_519

description: Hybridized to Axiom®_Exome_319


title: Blood_0_524

description: Hybridized to Axiom®_Exome_319


title: Blood_0_521

description: Hybridized to Axiom®_Exome_319


title: Blood_0_527

description: Hybridized to Axiom®_Exome_319


title: Blood_0_518

description: Hybridized to Axiom®_Exome_319


title: Blood_0_529

description: Hybridized to Axiom®_Exome_319


title: Blood_0_516

description: Hybridized to Axiom®_Exome_319


title: Blood_0_515

description: Hybridized to Axiom®_Exome_319


title: Blood_0_514

description: Hybridized to Axiom®_Exome_319


title: Blood_0_517

description: Hybridized to Axiom®_Exome_319


title: Blood_0_509

description: Hybridized to Axiom®_Exome_319


title: Blood_0_506

description: Hybridized to Axiom®_Exome_319


title: Blood_0_511

description: Hybridized to Axiom®_Exome_319


title: Blood_0_505

description: Hybridized to Axiom®_Exome_319


title: Blood_0_513

description: Hybridized to Axiom®_Exome_319


title: Blood_0_510

description: Hybridized to Axiom®_Exome_319


title: Blood_0_504

description: Hybridized to Axiom®_Exome_319


title: Blood_0_508

description: Hybridized to Axiom®_Exome_319


title: Blood_0_501

description: Hybridized to Axiom®_Exome_319


title: Blood_0_489

description: Hybridized to Axiom®_Exome_319


title: Blood_0_498

description: Hybridized to Axiom®_Exome_319


title: Blood_0_500

description: Hybridized to Axiom®_Exome_319


title: Blood_0_512

description: Hybridized to Axiom®_Exome_319


title: Blood_0_497

description: Hybridized to Axiom®_Exome_319


title: Blood_0_503

description: Hybridized to Axiom®_Exome_319


title: Blood_0_491

description: Hybridized to Axiom®_Exome_319


title: Blood_0_492

description: Hybridized to Axiom®_Exome_319


title: Blood_0_488

description: Hybridized to Axiom®_Exome_319


title: Blood_0_507

description: Hybridized to Axiom®_Exome_319


title: Blood_0_493

description: Hybridized to Axiom®_Exome_319


title: Blood_0_496

description: Hybridized to Axiom®_Exome_319


title: Blood_0_495

description: Hybridized to Axiom®_Exome_319


title: Blood_0_494

description: Hybridized to Axiom®_Exome_319


title: Blood_0_502

description: Hybridized to Axiom®_Exome_319


title: Blood_0_485

description: Hybridized to Axiom®_Exome_319


title: Blood_0_484

description: Hybridized to Axiom®_Exome_319


title: Blood_0_490

description: Hybridized to Axiom®_Exome_319


title: Blood_0_499

description: Hybridized to Axiom®_Exome_319


title: Blood_0_486

description: Hybridized to Axiom®_Exome_319


title: Blood_0_487

description: Hybridized to Axiom®_Exome_319


title: Blood_0_483

description: Hybridized to Axiom®_Exome_319


title: Blood_0_481

description: Hybridized to Axiom®_Exome_319


title: Blood_0_480

description: Hybridized to Axiom®_Exome_319


title: Blood_0_479

description: Hybridized to Axiom®_Exome_319


title: Blood_0_478

description: Hybridized to Axiom®_Exome_319


title: Blood_0_482

description: Hybridized to Axiom®_Exome_319


title: Blood_0_476

description: Hybridized to Axiom®_Exome_319


title: Blood_0_461

description: Hybridized to Axiom®_Exome_319


title: Blood_0_466

description: Hybridized to Axiom®_Exome_319


title: Blood_0_475

description: Hybridized to Axiom®_Exome_319


title: Blood_0_477

description: Hybridized to Axiom®_Exome_319


title: Blood_0_462

description: Hybridized to Axiom®_Exome_319


title: Blood_0_472

description: Hybridized to Axiom®_Exome_319


title: Blood_0_463

description: Hybridized to Axiom®_Exome_319


title: Blood_0_473

description: Hybridized to Axiom®_Exome_319


title: Blood_0_470

description: Hybridized to Axiom®_Exome_319


title: Blood_0_467

description: Hybridized to Axiom®_Exome_319


title: Blood_0_464

description: Hybridized to Axiom®_Exome_319


title: Blood_0_471

description: Hybridized to Axiom®_Exome_319


title: Blood_0_458

description: Hybridized to Axiom®_Exome_319


title: Blood_0_454

description: Hybridized to Axiom®_Exome_319


title: Blood_0_474

description: Hybridized to Axiom®_Exome_319


title: Blood_0_468

description: Hybridized to Axiom®_Exome_319


title: Blood_0_452

description: Hybridized to Axiom®_Exome_319


title: Blood_0_456

description: Hybridized to Axiom®_Exome_319


title: Blood_0_453

description: Hybridized to Axiom®_Exome_319


title: Blood_0_460

description: Hybridized to Axiom®_Exome_319


title: Blood_0_455

description: Hybridized to Axiom®_Exome_319


title: Blood_0_449

description: Hybridized to Axiom®_Exome_319


title: Blood_0_450

description: Hybridized to Axiom®_Exome_319


title: Blood_0_451

description: Hybridized to Axiom®_Exome_319


title: Blood_0_465

description: Hybridized to Axiom®_Exome_319


title: Blood_0_459

description: Hybridized to Axiom®_Exome_319


title: Blood_0_448

description: Hybridized to Axiom®_Exome_319


title: Blood_0_457

description: Hybridized to Axiom®_Exome_319


title: Blood_0_445

description: Hybridized to Axiom®_Exome_319


title: Blood_0_441

description: Hybridized to Axiom®_Exome_319


title: Blood_0_446

description: Hybridized to Axiom®_Exome_319


title: Blood_0_434

description: Hybridized to Axiom®_Exome_319


title: Blood_0_439

description: Hybridized to Axiom®_Exome_319


title: Blood_0_442

description: Hybridized to Axiom®_Exome_319


title: Blood_0_438

description: Hybridized to Axiom®_Exome_319


title: Blood_0_435

description: Hybridized to Axiom®_Exome_319


title: Blood_0_440

description: Hybridized to Axiom®_Exome_319


title: Blood_0_437

description: Hybridized to Axiom®_Exome_319


title: Blood_0_433

description: Hybridized to Axiom®_Exome_319


title: Blood_0_443

description: Hybridized to Axiom®_Exome_319


title: Blood_0_447

description: Hybridized to Axiom®_Exome_319


title: Blood_0_430

description: Hybridized to Axiom®_Exome_319


title: Blood_0_421

description: Hybridized to Axiom®_Exome_319


title: Blood_0_429

description: Hybridized to Axiom®_Exome_319


title: Blood_0_432

description: Hybridized to Axiom®_Exome_319


title: Blood_0_431

description: Hybridized to Axiom®_Exome_319


title: Blood_0_422

description: Hybridized to Axiom®_Exome_319


title: Blood_0_444

description: Hybridized to Axiom®_Exome_319


title: Blood_0_418

description: Hybridized to Axiom®_Exome_319


title: Blood_0_426

description: Hybridized to Axiom®_Exome_319


title: Blood_0_436

description: Hybridized to Axiom®_Exome_319


title: Blood_0_423

description: Hybridized to Axiom®_Exome_319


title: Blood_0_428

description: Hybridized to Axiom®_Exome_319


title: Blood_0_427

description: Hybridized to Axiom®_Exome_319


title: Blood_0_419

description: Hybridized to Axiom®_Exome_319


title: Blood_0_413

description: Hybridized to Axiom®_Exome_319


title: Blood_0_416

description: Hybridized to Axiom®_Exome_319


title: Blood_0_415

description: Hybridized to Axiom®_Exome_319


title: Blood_0_411

description: Hybridized to Axiom®_Exome_319


title: Blood_0_414

description: Hybridized to Axiom®_Exome_319


title: Blood_0_408

description: Hybridized to Axiom®_Exome_319


title: Blood_0_420

description: Hybridized to Axiom®_Exome_319


title: Blood_0_417

description: Hybridized to Axiom®_Exome_319


title: Blood_0_403

description: Hybridized to Axiom®_Exome_319


title: Blood_0_410

description: Hybridized to Axiom®_Exome_319